I don't find the alien base missions that bad tbh. Just a case of going super carefully and building a fire team with good acc from a decent postion and using another sparsely equipped unit with lots of movement as the spotter. As I'm sure has been said you use that unit to poke his/her head in, get a bead on em and lay down some doom with -in my case- a couple of rockets and an opening barrage of burst then a few well placed aimed shots. Also lots of moving out of cover to take a shot then slipping back into it is a must. It does mean each base run takes a while though!
