1. Aliens should not forget where your base is without good reason.
Good reason is you built a mindshield.
Decent reason should be you destroyed a bunch of bases in the area.
2. When aliens retaliate, they should do it en mass.
As soon as a retaliation mission is triggered (ie that scout is looking for your base), the game should generate multiple battleship attacking all known bases. If the scout finds another base, then another round of all your known bases being attacked by multiple alien ships.
The aliens are suppose to have unlimited resources, they should use them.
3. Battleships or a new larger capital ship should have the ability to bombard your base while you defend it.
If you have no base defenses, aliens win automatically.
Assuming you do have base defenses, every 10 turns, the alien ship takes a blind shot that could destroy a whole room. There should be a certain chance that the alien's bombardment fails to get through. Meanwhile, so long as you have base defenses, they get to keep shooting at the Alien ship.
4. Multiple ships means multiple waves of invaders.