People just don't like "XCOM" because it comes from another game and that's it. It has nothing to do with realism, plausibility, being too abstract, or anything else. They just don't like the reference being made.
Admittedly, there is more variety in the complaints than that. Certainly, there have been those that felt it's an advertising gimmick, although whenever I think of "X-Com" I think of the 1990s Microprose game, so I can't help but think of it as an homage to a classic from the same company that made the original Civ, and not an advertising spiel for the recent reboot.
There's also been complaints about the canonicity of the X-Com concept, in that aliens have never appeared in the Civilization universe (as opposed to, say, SimCity where one could fight off mutant monsters and alien invasions). Although it is curious to wonder how these people feel about the Alpha Centauri franchise, which
did have canon aliens. Is Alpha Centauri part of the Civilization canon?
Many of the other complaints have largely revolved around the perception of Civilization as a serious historical simulation game. There are those who argue that Civilization should be purely about
history, and thus not feature any elements from the future (which makes me wonder how they feel about technologies like "Fusion" that aren't viable yet). Snoopaloop (as an example) complains that futuristic elements ruin the sense of immersion in historical gameplay. There are also those who feel that less-than-serious elements such as the GDR and X-Com Squad are too whimsical for the game, presumably feeling that the game should be more serious in tone.
I was just somewhat bemused because nearly all of these complaints can be applied to the spaceship project, as well. We're nowhere near making a viable starship -- heck, even reaching
Mars likely won't occur for a decade or two, at least. It's a whimsical reference to another game series that takes place using fictional, fantastic technologies in the future, rather than history. It's basically like every single complaint wrapped up into a single package. X3 And yet, most people go "Oh, it's part of the game, so I accept it". It seems oddly dissonant.
Who knows, perhaps in Civ 6 we'll see a more appropriate science victory -- I still think building the LHC and discovering the Higgs Boson would be a better conclusion for it, and would fit more with the "historical simulation" concept.
On the other hand, in the end it's Firaxis' game to make and they'll choose what to include or not based on their own vision. I suspect most of the complaints are really because everyone has their own personal interpretation of what the game
should be, and given the opportunity they'd probably go "Hey Firaxis, make the game
I want, not the game
you want to make."