An idea we discussed some time ago on IRC was to rework the way that the reactor and the overmind attacked enemy players inside of the base. For the most part, they don't really do a lot of damage unless you're an unarmored human or a small alien. The idea would be to change it so that the structures have very powerful attacks, but that these attacks get split up if multiple opponents are nearby. For instance, one opponent could be fried for up to 80 damage, two opponents would receive 40 damage, four would receive 20 damage, and so on and so forth. The exact numbers don't matter as much as the idea that bases would have an easier time fending off lone wolf attackers while at the same time encouraging team rushes into bases.
Beyond that, I'm interested in some small secondary things as well. If the reactor attacks via bolts of lightning, why not have it arc across aliens like the mara zap? As for the overmind, how about having it distort your vision and disrupt your audio? Not enough to have a game-changing effect, but instead something that makes it much more scary to new players than it actually is.
Other ideas are also welcome here, of course.