I first started reading this thinking it was a crap idea. But I'm thinking something of the like could help a lot.
The problem is, rarely does the alien team camp, because their defense isn't effective enough for that. And since their defense is melee and best placed behind doors, humans would be able to build their base attacker by simply clustering around it as it builds behind the door to the alien base. Then boom, the defense is gone, and the humans rush in. And only having it for the alien side would be cheap, especially if it's hidden somewhere hard to reach.
But the building-to-building concept is an interesting one. I think it should be something that only works by LoS, a complete 3d one would have lots of balance issues. (Think, you could put one on the floor directly above the enemy base and destroy everything before they know what hit them)
Now, I'd imagine the human one as resembling a repeater (compact, rounded shape), and it temporarily disables buildings by hitting them with a tesla-like zap that does little damage, and disables the structure for maybe 10 seconds. The defense computer would make these structures target all structures in range in sequence instead of repeatedly hitting the closest one, which would end up disabling many more structures. And of course it would have the hp of an armoury, so that they're only useful when the humans are dominating and can defend such a forward structure.
The aliens would have basically the same thing, but I can't be bothered to think of an organic attack that would incapacitate buildings but not units.
By limiting it to a short line-of-sight range, it makes them only effective when the team is doing well anyway. However imo it'd be far less easy to abuse.
