I think it would be a nice idea if a building like a turret for example, after taking some damage, it starts firing slowler, and a damaged reactor would provide less energy. And also, after a new stage, the build points should increase.
Oh and BTW you should realy make a BFG kinda weapon, like the lucifer cannon =)

Thats a great idea! 

Less efectivity for damaged  buildings: I think that it would be too hard for humans.

New stage = more BP: That is possible. I think it would be good as server option and it can reduce camping in some cases.

BFG: (bazooka ) It is hard or impossible to make such weapon balanced. That is reason why we do not plannig it. But you will be able to use similar weapons in some maps - only you can't to pick up them and carry them away - you have to use it on that place. Something like this for example:

WOW
I like that =P
Another thing I though would be cool is to make some new ways to generate more power for humans and aliens, for example
Reactor/Slave Worker - Generates power out of nowhere for the starting game
Solar Synthesizer/Alien photosynthesis - Generate a small boost of energy for the base
Control Center/Overmind - Controls every machine/alien building, and if destroyed, everything stops working (like the actual Reactor/OM)
Laser Turret/Fire ball launcher - Sets enemys on fire from a distance

I know the names suck, but the idea sounds nice, to have more buildings =D

More buildings is good, we have few of new buildings in plans. But need to be tested and balanced. We do not want to create strategy game from it