Thanks for bringing this one up ben_danger. I've been mulling this one over for quite a while myself.
I think the big Droid Control ship from Episode 1 is probably the most suitable to be a "bad guys' base" ship, and it's the most realistic part of the whole prequels as it was actually an enormous miniature they built.
Add to that the fact we already have some footage of it being blown up which can be utilised for Episode 3 when they're finally defeated.
If a radical editor wanted to completely redo the concept, or have a completely different stationary base, the Space Station in the game Knights Of The Old Republic would be a good reference, plus possibly provide some good ideas:
As well as the aesthetic of it drawing its power direct from a star (pretty cool) this space station was called the 'Star Forge' and was essentially a giant space factory. It is how the Sith in the game were able to churn out seemingly impossible numbers of ships and droids. This is a concept that could easily be adapted for our Prequels with the Droids army and droid ships.
More radical still, if someone wanted Clones on the opposing side (me me me me!), it could replace Kamino and explain the overwhelming amount of troops the opposition has. The almost decimated Republic must then, just for survival, mount a last ditch assault on this newly discovered threat, and we then have the moral issue of our supposed good guys extinguishing millions of lives in the process, thus making an obvious parallel with Alderaan. We could have all the Jedi back on Coruscant feel the disturbance in the force just like Obi Wan did in ANH. The act would speak for itself. The Republic is becoming evil.
The last thing I would want though is for someone to interpret this act of evil as a Pro-Life/Anti-Abortion message. Destroying a space station full of largely embryonic humans, and then becoming the Evil Empire? LOL. It seems almost too perfect doesn't it? Honestly though, it's just an accident that the idea has those parallels. I don't have an agenda, certainly not that one as I'd be considered 'Pro Choice'.