First base is turned into research facility (6 labs in the end, workshop demolished)
Second is a factory (used to get basic equipment asap, than to dissemble alien ships) - 6 workshops, no missile defenses (but 4 external), no ships.
3rd is more balanced, with some extra storage space, another drop-ship with "backup" team, single laboratory, workshop and alien storage.
4+ are just used to stop alien ships (interceptors, base defenses, a workshop or two to maintain production of ammo for my soldiers).
My combat teams are composed of:
a) 4-5 laser weapon users (any, but rifles work best)
b) 1-2 GL with few extra plasma blades
c) 1-2 Railgun
I set team a) in a far, but very visible spot, to attract fire and get some reaction kills eventually, while being relatively safe (sometimes some healing is required, but rarely ever any soldier dies).
Team b), hidden behind corners, is used to stop enemies from flanking, and to do final charge. They also serve as medics during long-range combat, or can help with RL (in backpacks).
Team c) usually gets to the building / behind the wall etc, and kills everything in range trough the walls, using infrared goggles.
For some reason (lousy path finding?) some enemies won't leave ships/buildings. Some also play a variant of hide-and-shoot without actually ever shooting (lack of TU). Also, quite often, they keep trying to shoot you trough the wall. That is when snipers/railgunners come handy.
I've noticed that AI engages in long-range combat first with ~half of the units, than sends some to flank/rear your soldiers, so my game style is just a countermeasure.
Until strength is implemented, every soldier carries a first aid kit, at least one plasma blade, spare ammo and an alternative weapon in the backpack (stun rod for a), RL for b), laser rifle for c) ).