I think something that should be included is alien ships performing an orbital bombardment. I might even suggest they create a new class of ships which can do this (have the current battleship be reclassified as a battlecruiser and the new ship be the battleship).
Right now, the player either has a grav shield and a few fusion launchers that destroys almost any attacking ship or has a base layout that makes a super chokepiont that the aliens run head long into.
To change this up, have an alien attack force from this new ship that has its aggression level turned down by 1, which should make some of the aliens play only defense. Meanwhile every 5 or 10 turns, the ship performs an orbital attack that destroys everything in a room, possibly the room itself as well. These attacks could either be semi random (no attacks on hangar bays or the access lift) or called down by an alien spotting a human. If you have a single missle launcher, then every 5 or 10 turns, you get another attack on the ship while the base defense is going on
Other minor changes, let the aliens spawn in defense systems since they must be close to the surface.
