A prospect I've been interested in as of late is the concept of a "Warhammer 40k X-COM". I started noticing the parallels some time ago, and I just keep finding more and more...
First, you got your grunts. The guys equipped with coveralls and laser rifles because you can't be arsed to give them anything more expensive until they've proven themselves. Does this sound at all like the "T-shirt and flashlight" of the Imperial Guard? Heck, you can even make it a pistol for more shots and worse damage, if you like.
On their own, they're pretty much just fodder. But the Imperial Guard has always been known for its array of heavy weapons platforms, which gives them the armored support they need to win the day. Got a trickier problem on your hands? Toss a psyker out into the mix!
The aliens are obviously various members of the T'au coalition. A vast array of different races pulled together to serve under one purpose, all under the guiding hand of the Ethereals (bonus points: check the autopsy report for ethereals, where they take the cloak off. Does that tall, skinny alien with peculiarly-shaped head and slightly blueish skin look at all familiar?)
This kind of alien scum can obviously only be dealt with by the great space marines, with their power armor and heavy plasma rifles, they wield the divine power of the emperor against the alien threat. If you want them to have heavy bolters instead, just hook 'em up with an autocannon and explosive rounds (or AP, if you for some reason don't want massive amounts of collateral damage).
Should the enemy prove altogether too mobile and sneaky, send in a shock team of assault marines with flight suits, plasma pistols, grenades and stunsticks.