There are smaller boards like Nano. It too has 6 PWM outputs 
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You could use a standalone microcontroller, such as ATtiny45 or similar. It's true to the name and really is tiny (only 8 pins, two of which are PWM).
Yes, there are Arduino simulators out there, but I haven't used them really and since I have a few boards, I can always test stuff directly so I don't need them. You may find them useful until you get an actual board, though.