As others have mentioned in others posts, base attacks really need to be reworked or changed. But i'm really of the opinion that it should be changed ASAP because right now it really sours my game experience. I love X2 and what they have done so far, but base attacks mechanics are irritably boring, unfair and poorly designed as it is.
For having played a few, when a base attack come up i don't even bother anymore and just cheat the mission and win it instant.
You have no idea how enraging it is when you have a so many things to do and get done, as well as manage your strike teams only to have a BS base attack come up from nowhere. They don't even make sense because if the aliens know your base locations, why would they even bother invading it at all and not just delete it with an orbital strike from outer space? They can already destroy huge population centers with it, certainly they can spare an orbital shot on what is arguably their greatest nuisance.
The old system where it was a UFO that could be intercepted was perfectly fine and allowed players multiples layers of protection for their main base and to cover their secondary ones with air forces.
I get it, you want players to explore the experience of base attacks, something some X1 players never experienced because they could always intercept the UFO's before they could get close. That doesn't mean you should force it upon players with an unavoidable, unskippable and nonsensical base attack mission that cannot in any way be intercepted or prevented in some manner before it happens.
Here are the main issues, and my suggestions:
1. Unavoidable. By far the biggest issue. Base attacks will happen no matter how good or how poor your performance was. You can't intercept the UFO's, the missions doesn't happen out of failure of achieving a requisite (Such as a specific mission type where aliens gather information in a military/government facility, which would compromise the location of your base) and there are no warnings beforehand (Such as an anonymous tip that someone fear your NA base will be attacked in 48 hours).
Fixing this is relatively simple; revert to an X1 system where it was interceptable UFO's with base attacks missions. If you fail to intercept the UFO before it reaches your bases, then it's fair to have a base attack mission. If you want to force players to experience a base attack mission in their playthrough at least once, you could make a specific event tied to cleaners chain missions early game; for example, when you kill/capture the VIP cleaner in that ambush mission, Cleaners could stage up an assault in your base in an attempt to either free the VIP (If you captured him) or in retaliation to his death. It would make a lot more sense and serve to introduce new players to base attacks mechanics, and remind them of the dangers of having your bases attacked and place soldiers and equipment in order to defend your bases.
It could also introduce the possibility of adding specific UFO's designed for base invasions, that could be stealthy and fast, in order to reduce your likelihood of interception. Or specific missions to protect your base location, etc... All kind of possibilities.
2. Lack of overwatch for the initial alien turn. You can already place your soldiers anywhere in your base (except where the rooms where aliens are), so that means that your soldiers are already in position and ready to fight. So there is no reasons none of them shoot the crap out of them when they come out of the doors during the initial alien turn. Having a perfect setup of machine guns and shotguns on standby by the door only for them to get blasted to hell because none have overwatched is really dumb.
3. This one is quite much more minor. Lack of base interactions for both aliens and player. It's your base, but you can't figure out where they are by using cameras, lock doors, place traps, etc... That would be way more interesting if you had more abilities like these. Perhaps it would be worth introducing a security room from where you need a xenonaut to be present in order to see the camera feeds, and the cameras could be shot down by aliens as well. Locked doors could be blown or shot open. Said security room could add bonuses such as the already mentioned cameras, free friendly security soldiers and pre-placed traps.
Invasions could be then re-balanced with more powerful aliens forces, either by numbers or equipment, to keep it challenging.
But i understand it would require quite an extensive amount of time and efforts to add those, so this one is merely an idea more than anything.