This was a bad idea since almost all stack-based languages look unreadable (look at Jelly).
But here goes:

This was a bad idea since almost all esoteric languages look unreadable (look at Jelly).
But here goes:

Pylongolf2 beta5

) Print the stack.
Ü Toggle the method Pylongolf2 uses for pushing to stack.
a The useless command, removes and adds the selected item in the same place.
c Ask for input.
n Convert string to a number.
" Toggle string mode for pushing text to the stack.
s Convert a number to a string. ╨ Encode the selected item (it must be a string).
_ Duplicate the selected item next to itself.
b Swap places between the selected item and the one before.
d Set the selected item to the last one.
m Move the selected item to the end of the stack.
@ Select an item. (Number required after this command as an argument).
w Wait a specified amount of time (the time is taken from the stack).
= Compare the selected item to the one before. (WARNING. THIS DELETES THE 2 ITEMS AND PLACES A true OR A false) (V2 beta)
~ Print the stack nicely. (V2 beta)
² Square a number. (V3 beta)
| Split a string to an array by the character after |. (V4 beta)
♀ Pop the array. (the contents are left in the stack) (V4 beta)
> Begin a while statement. (V5 beta)
< Loop back to the beginning of the while statement. (V5 beta)
! Break out of the while statements. (V5 beta)

Pylongolf2 beta6

) Print the stack.
Ü Toggle the method Pylongolf2 uses for pushing to stack.
a The useless command, removes and adds the selected item in the same place.
c Ask for input.
n Convert string to a number.
" Toggle string mode for pushing text to the stack.
s Convert a number to a string. ╨ Encode the selected item (it must be a string).
_ Duplicate the selected item next to itself.
b Swap places between the selected item and the one before.
d Set the selected item to the last one.
m Move the selected item to the end of the stack.
@ Select an item. (Number required after this command as an argument).
w Wait a specified amount of time (the time is taken from the stack).
= Compare the selected item to the one before. (WARNING. THIS DELETES THE 2 ITEMS AND PLACES A true OR A false) (V2 beta)
~ Print the stack nicely. (V2 beta)
² Square a number. (V3 beta)
| Split a string to an array by the character after |. (V4 beta)
♀ Pop the array. (the contents are left in the stack) (V4 beta)
> Begin a while statement. (V5 beta)
< Loop back to the beginning of the while statement. (V5 beta)
! Break out of the while statements. (V5 beta)
? An if statement, does nothing if the selected item is a `true` boolean. (V6 beta)
¿ If an if statement is `false`, the interpreter skips everything to this character. (V6 beta)

If Statements

To do if statements, put a = to compare the selected item and the one after.
This places either a true or a false in it's place.
The command ? checks this boolean.
If it's true then it does nothing and the interpreter goes on.
If it's false then the interpreter skips to the closest ¿ character.

Interpreter for Pylongolf2 (Java):

package org.midnightas.pylongolf2;

import java.io.File;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Random;
import java.util.Scanner;

public class Pylongolf {

    public static final void main(String[] args) throws Exception {
        String content = new String(Files.readAllBytes(Paths.get(new File(args[0]).toURI()))) + " ";
        boolean fullreadMode = true;
        List<Object> stack = new ArrayList<Object>();
        List<Integer> whileStatements = new ArrayList<Integer>();
        HashMap<String, Object> vars = new HashMap<String, Object>();
        int ifStatements = 0;
        Scanner scanner = new Scanner(new UnclosableDecorator(System.in));
        int selectedIndex = 0;
        for (int cl = 0; cl < content.length(); cl++) {
            char c = content.charAt(cl);
            if (isNumber(c)) {
                if (!fullreadMode) {
                    stack.add(Double.parseDouble(c + ""));
                } else {
                    String number = "";
                    for (int cl0 = cl; cl0 < content.length(); cl0++) {
                        if (isNumber(content.charAt(cl0))) {
                            number += content.charAt(cl0);
                        } else {
                            cl = cl0 - 1;
                            stack.add(Double.parseDouble(number));
                            break;
                        }
                    }
                }
            } else if (c == ')') {
                System.out.println(Arrays.toString(stack.toArray()));
            } else if (c == 'Ü') {
                fullreadMode = !fullreadMode;
            } else if (c == '+') {
                if (stack.get(selectedIndex) instanceof Object[]) {
                    Object[] obj = (Object[]) stack.remove(selectedIndex);
                    Double dbl = new Double(0d);
                    for (Object o : obj) {
                        dbl += (Double) o;
                    }
                    stack.add(selectedIndex, dbl);
                } else {
                    Object obj0 = stack.remove(selectedIndex);
                    Object obj1 = stack.remove(selectedIndex);
                    if (obj0 instanceof Number && obj1 instanceof Number)
                        stack.add(((Number) obj0).doubleValue() + ((Number) obj1).doubleValue());
                    else if (obj0 instanceof String) {
                        stack.add(obj0.toString() + obj1.toString());
                    }
                }
            } else if (c == '-') {
                Object obj0 = stack.remove(selectedIndex);
                Object obj1 = stack.remove(selectedIndex);
                if (obj0 instanceof Number && obj1 instanceof Number)
                    stack.add(((Number) obj0).doubleValue() - ((Number) obj1).doubleValue());
                else if (obj0 instanceof String && obj1 instanceof String) {
                    stack.add(obj0.toString().replaceAll(obj1.toString(), ""));
                }
            } else if (c == '*') {
                Object obj0 = stack.remove(selectedIndex);
                Object obj1 = stack.remove(selectedIndex);
                if (obj0 instanceof Number && obj1 instanceof Number)
                    stack.add(((Number) obj0).doubleValue() * ((Number) obj1).doubleValue());
            } else if (c == '/') {
                Object obj0 = stack.remove(selectedIndex);
                Object obj1 = stack.remove(selectedIndex);
                if (obj0 instanceof Number && obj1 instanceof Number)
                    stack.add(((Number) obj0).doubleValue() / ((Number) obj1).doubleValue());
            } else if (c == 'a') {
                stack.add(selectedIndex, stack.remove(selectedIndex));
            } else if (c == 'c') {
                stack.add(scanner.nextLine());
            } else if (c == 'n') {
                if (stack.get(selectedIndex) instanceof String) {
                    stack.add(selectedIndex, Double.parseDouble(stack.remove(selectedIndex).toString()));
                } else if (stack.get(selectedIndex) instanceof Object[]) {
                    Object[] oldArray = (Object[]) stack.remove(selectedIndex);
                    Object[] newArray = new Object[oldArray.length];
                    for (int i = 0; i < oldArray.length; i++) {
                        newArray[i] = Double.parseDouble(oldArray[i].toString());
                    }
                    stack.add(selectedIndex, newArray);
                }
            } else if (c == '"') {
                String string = "\"";
                for (int cl0 = cl + 1; cl0 < content.length(); cl0++) {
                    string = string + content.charAt(cl0);
                    if (content.charAt(cl0) == '"') {
                        stack.add(string.substring(1, string.length() - 1));
                        cl = cl0;
                        break;
                    }
                }
            } else if (c == 's') {
                Object obj = stack.remove(selectedIndex);
                if (obj instanceof Double) {
                    Double dbl = (Double) obj;
                    if (dbl.doubleValue() == Math.floor(dbl)) {
                        stack.add(selectedIndex, "" + dbl.intValue() + "");
                    } else {
                        stack.add(selectedIndex, "" + dbl + "");
                    }
                }
            } else if (c == '╨') {
                cl++;
                char editmode = content.charAt(cl);
                if (editmode == '0') {
                    stack.add(selectedIndex, rot13(stack.remove(selectedIndex).toString()));
                } else if (editmode == '1') {
                    stack.add(selectedIndex,
                            new StringBuilder(stack.remove(selectedIndex).toString()).reverse().toString());
                } else if (editmode == '2') {
                    stack.add(selectedIndex, stack.remove(selectedIndex).toString().toLowerCase());
                } else if (editmode == '3') {
                    stack.add(selectedIndex, stack.remove(selectedIndex).toString().toUpperCase());
                }
            } else if (c == '_') {
                stack.add(selectedIndex, stack.get(selectedIndex));
            } else if (c == 'b') {
                stack.add(selectedIndex + 1, stack.remove(selectedIndex));
            } else if (c == 'd') {
                selectedIndex = stack.size() == 0 ? 0 : stack.size() - 1;
            } else if (c == 'm') {
                stack.add(stack.remove(selectedIndex));
            } else if (c == '@') {
                String number = "";
                for (int cl0 = cl + 1; cl0 < content.length(); cl0++) {
                    if (isNumber(content.charAt(cl0)))
                        number += content.charAt(cl0);
                    else {
                        cl = cl0 - 1;
                        selectedIndex = Integer.parseInt(number);
                        break;
                    }
                }
            } else if (c == 'w') {
                String number = "";
                for (int cl0 = cl + 1; cl0 < content.length(); cl0++) {
                    if (isNumber(content.charAt(cl0)))
                        number += content.charAt(cl0);
                    else {
                        cl = cl0 - 1;
                        Thread.sleep(Long.parseLong(number));
                        break;
                    }
                }
            } else if (c == '=') {
                Object obj0 = stack.remove(selectedIndex);
                Object obj1 = stack.remove(selectedIndex);
                stack.add(new Boolean(obj0.equals(obj1)));
            } else if (c == '~') {
                for (Object o : stack)
                    System.out.print(o);
                System.out.println();
            } else if (c == '²') {
                if (stack.get(selectedIndex) instanceof Double) {
                    Double dbl = (Double) stack.remove(selectedIndex);
                    stack.add(selectedIndex, dbl * dbl);
                } else if (stack.get(selectedIndex) instanceof Object[]) {
                    Object[] obj = (Object[]) stack.remove(selectedIndex);
                    Object[] newArray = new Object[obj.length];
                    for (int i = 0; i < obj.length; i++) {
                        newArray[i] = Math.pow((Double) obj[i], 2);
                    }
                    stack.add((Object[]) newArray);
                }
            } else if (c == '|') {
                String string = (String) stack.remove(selectedIndex);
                cl++;
                char splitChar = content.charAt(cl);
                stack.add((Object[]) string.split(splitChar + ""));
            } else if (c == '♀') {
                for (Object obj : (Object[]) stack.remove(selectedIndex)) {
                    stack.add(selectedIndex, obj);
                }
            } else if (c == '>') {
                whileStatements.add(new Integer(cl));
            } else if (c == '<') {
                cl = whileStatements.get(whileStatements.size() - 1);
            } else if (c == '!') {
                whileStatements.remove(whileStatements.size() - 1);
            } else if (c == '?') {
                if (stack.get(selectedIndex) instanceof Boolean) {
                    Boolean bool = (Boolean) stack.remove(selectedIndex);
                    if (bool == false) {
                        ifStatements++;
                        for (int cl0 = cl; cl0 < content.length(); cl0++) {
                            if (content.charAt(cl0) == '¿') {
                                ifStatements--;
                                cl = cl0;
                            }
                        }
                    }
                }
            } else if (c == 't') {
                break;
            } else if (c == '(') {
                stack.remove(selectedIndex);
            } else if (c == ':') {
                cl++;
                char charToVar = content.charAt(cl);
                vars.put(charToVar + "", stack.remove(selectedIndex));
            } else if (c >= 'A' && c <= 'Z') {
                stack.add(vars.get(c + ""));
            } else if (c == 'r') {
                stack.add(selectedIndex,
                        (double) new Random().nextInt(((Double) stack.remove(selectedIndex)).intValue() + 1));
            }
        }
        scanner.close();
    }

    public static String rot13(String input) {
        StringBuilder sb = new StringBuilder();
        for (int i = 0; i < input.length(); i++) {
            char c = input.charAt(i);
            if (c >= 'a' && c <= 'm')
                c += 13;
            else if (c >= 'A' && c <= 'M')
                c += 13;
            else if (c >= 'n' && c <= 'z')
                c -= 13;
            else if (c >= 'N' && c <= 'Z')
                c -= 13;
            sb.append(c);
        }
        return sb.toString();
    }

    public static boolean isNumber(char c) {
        return c >= '0' && c <= '9';
    }

}