The aliens really hurt the atmosphere. I've always thought, that the story behind AC was quite intelligent. It tries to be minimalistic and stresses the conflicts and the suspense between the characters. That's a major part of the story: interacting characters. In that regard, it was not mainly a Sci-Fi plot, but a story about these factions colonizing new terrain. Introducing aliens just ruins it and does not make sense. Where have they been, why did they leave?
Apart from that, some secret projects are questionable and the introduction of more indigenous life-forms was unnecessary. A few bugs have been fixed, but fan-made patches would do the same. I think Alien Crossfire also runs technically better. I wasn't able to run AC on XP in a different resolution without a battered interface. I don't remember it perfectly. I also had to manipulate language files by myself, because the patch is exclusively in English.
Mekonis: I've never seen a community so divided on an expansion. Expansions are usually considered as must haves.
Nope, so many add-ons of acclaimed titles were utter trash, due to people leaving the team, conflicts between publishers and developers and so on. They often threw lots and lots of new scenarios at you without a nice campaign in the style of its main game. I remember Red Alert having only average expansions. The Deeper Dungeons did not have its main campaign speaker. Shadow of Death received mediocre critics. The Total Annihilation add-ons were deteriorating in campaign quality, too. And don't forget garbage like all of those The Sims continuations.