Exactly - what many people remember from the original X-Com are those experiences and the atmosphere. Everyone of my colleagues and friends, who played the original X-Com, first talk about the creepy corn fields at night. And when it comes to X-Com: TFTD it is something like that:
"The music + late night playing with no lights + alien base missions + high volume sonic cannon shots and aquanaut screams + tentaculats = the definition of terrifying"
It is also the atmosphere and the "experience" that attracts a lot of people when it comes to games; not perfect gameplay mechanisms and balancing down to the smallest detail. It is about how it "feels" to play.
The graphical presentation is a part of this: I love the sober mil-sim look of X2, but more darkness and things like fog could greatly increase how the game feels. For example: the alien bases would be much more atmospheric if they would be dark and maybe filled with fog (the alien creatures having their own atmosphere in there). "Darkwood" or "Aliens: Dark Descent" (aka X-Com: Colonial Marines) do it nice, albeit a little bit too much of everything. A more "sober" approach like in X2 would be better.
And equally much can be achieved with game features: keeping the enemy creatures as "unknown" as possible (no status messages for the creatures: HP, "suppressed" etc.). A nice little, immersive gadget: a separate "motion sensor" (very atmospheric to have to use it and draw conclusions), presenting a motion sensor with overlay UI (something flashes on the virtual battlefield), on the other hand, is not atmospheric at all. This creates memorable experiences and is immersive/atmospheric ("What moves there in the darkness/inside the barn/house etc.):
https://www.ufopaedia.org/index.php/File:Xenomorphs.png
What players often remember most about games, the most memorable experiences, seem to be the "levels"/"missions"/etc. that they had to go through despite being hard (and dark and scary): Everyone talks about the "Tower of Latria" or having to climb down into the "Valley of Defilement" in Demons Souls, or "Blighttown" in Dark Souls. Same for the original X-Com: those atmospheric night missions, going through the cornfields...
X2 is a game about alien creatures and the "unknown" (and not something like "Jagged Alliance") - so darkness and creating an overall eerie atmosphere would really fit imho.