With everyone saying "Off with their heads!" - oops, I mean "Off with the limits!", I hate to be a nay-sayer.
I'd like to see the original limits still in place. You need a power room to put a power generator, a teleport room to put in your teleporters, etc.
Personally, I think you could put enough in to make it slow as heck, but why do that? And, if there's a "memory leak" - why push it to crash the game? And, if one-day we get the game back, it would be nice to have practiced the game with the original limits in place. And let people see what they could build with those limits. Maybe even put in a limit that you can't have both Paragon City and Rogue Islands beacons to be a Hero or Villain base.
Now, this version would should let you just buy anything, even though you haven't earned the badges (you can't earn badges right now), but let people see what they can build. Maybe even keep a record of Prestige spent. This way, you can see what you'd need to build your "ultimate base". For me, it was to get the base functional (a functional teleporter to each zone, functional medical bay, etc.) and then let my friend decorate to his heart's content. Actually, this was sometimes a contention between us - I'd save Prestige to build something in the base, and my friend would see that prestige just sitting there and start decorating like mad and buying decorative rooms. Eventually, we agreed that I would get everything functional, and then he could decorate when I'm done. So we'd end up with everything that we need operationally near the entrance (workroom/teleport/medical) and then he could add whatever else he wanted. It made for a nice base.
