well lets face it civ... if the marines get 2 hives locked down, it's usually game over for the aliens or as good as, I don't see why having the aliens beat back the marines to get all 3 hives is much different.
Marines don't have to fight for territory for their tech tree... all they need is the res. Ok so that means res nodes but aliens already have to fight for that too, nevermind the hives. Unlike the aliens a marine at top tech can be done without fighting over the hives, while the aliens HAVE to capture x amount of hives to gain a full tech tree so trying to compare the two as top tech levels isn't really fully feasible =/
it's genuinely harder for the aliens to achieve conquering and holding 3 vital areas, while the marines simply need time and res (something the aliens have to worry about ontop of the whole hive thing).
Back in 1.04 third hive was as good as game over, I remember reading somewhere that the reason they allowed the other lifeforms outside of their respective hive limits in later versions was to allow players to experience the whole spectrum of alien lifeforms and bring more diversity to them rather than any form of actual balancing. I personally take that as a sign that 3 hive aliens have earned a win, just as 3 hive marines do =P
heck, maybe they should just the marines at one of the hives. that way you're at least guaranteed a fight for the 3rd one.