I've had two ideas recently that can easily be implemented. Tell me what you think. If enough people like them, and they work, they can be in-game soon. Feel free to suggest changes to them, too.
My idea for the defense computer is that in addition to its current role of providing regeneration and warning of attack, it can also hide buildings around it from alien detection. Thus, they do not appear as blips on the alien "radar" while they're moving around. Humans can also be concealed. Of course, you and your buildings can still be seen and heard, you haven't gone invisible. I believe that this could make later stages much more interesting, as your repeater outposts can include a medistation and a defense computer now, providing you with a stealthy recharge station for energy weapons. It could also help conceal mid-game base movements from rampaging aliens.
As for the marauder zap, I was thinking that instead of doing direct damage, it can do EMP instead. Thus, when you zap a structure, it's temporarily disabled. This would still allow a group of marauders to take apart a base, but you'd have to do it in a different fashion now, taking apart the defense structures before they function again. This could possibly work on humans in battlesuits too, allowing for the marauder to be more effective against stage 3 humans that can easily kill it with a single lucifer cannon shot.