I want to start a Quadrupod using an Arduino and a SSC-32 to control 12 servos. I was wondering Arduino should I use, I was thinking either the Mega or the Due. The main difference seems to be the operating voltage, the Due uses 3.3v compared to the Mega's 5v. What would be the best?
I don't think "best" is the right word here; even a standard Arduino Uno would work fine for controlling the quadruped since you intend to use an SSC for the servos (smart choice, BTW). The real question is - what do you intend to do with this quad? That is - what kind of sensors, what kind of programming, etc do you intend to use?
I mean - if all you wanted to do was to have the thing walk around, avoiding obstacles using a scanning ultrasonic sensor, etc - you could easily do that with an Uno. If, however, you wanted to play with AI routines, (simple) SLAM, etc - and have more sensors, etc - correlate data, and so on - well, a Due might be the better approach. As for a Mega - that would fall somewhere in the middle.
In other words, you've given us a concept - but not a spec of what you want to do; without those specifics, a good recommendation would be difficult to make. For us to hedge our bets, I would have to suggest going for the most powerful device you can afford (an NVidia Tesla connected via WiFi should work OK)...
As for interfacing the Due - as long as the SSC can work with a 3.3 volt serial TTL comms, it should be ok - otherwise, you might need to add some simple level shifting.