If you are concerned that you don't have enough pins, try looking here:
This guy is controlling 768 LED’s at 32 brightness levels using just 3 pins of an Arduino - an Uno would be fine for this. Even a 'Mega doesn't have quite that many pins - you just need to learn what's out there and how to use it.
Unless you know that what you want to do can't be easily achieved with external driver/shift-register type chips then I would start with an Uno. And as DuaneB says, once I have something I like, I build it with a dedicated '328 chip on a bit of circuit board so that I can keep it forever. The controller actually only costs £3-4 so you can trial a project with your 'Uno and then once you have what you like you can make a permanent version. You can't do that easily with a 'Mega because the 2560 controller is a 100-pin surface mount package only.
For $150 you could do loads of fun things with an Uno and a bunch of peripheral items, especially if you work up enough understanding to build a few $10 boards of your own - it's really not hard.