Praetoria was one of the things I never got around to exploring in the game. Mostly because I don't really like the "evil parallel world" story conceit (unless everybody evil wears goatees 
) And on my earlier machine, I found the environment gave my clunky build some problems with clunky rendering.
I'll try and do a real run through as one of my celebratory explorations when we get the game back.
I think you are only locked out of SG's and such until you hit 20. Once you choose a side you can access them, just not easily from Pretoria.
If we could have made changes to bases, it would have been nice to add a portal ala portal corp in the bases that could take you to Pretoria. Or maybe even teleport beacons. I think more integration and story diversification and Pretoria would have been incredible. Imagine stories that don't revolve around Emperor Cole and the fight against him.
Some DE attacking refugee camps would have been perfectly in line and would let heroes do their thing. Even Villains could have joined in as they could open the shields, let the DE in and clean the place out in the confusion, maybe kidnap a key leader or recover someone who fled to escape the wrath of Arachnos.
