Again...I'm not a comic book guy so I'm just going off of what the movies have given us (plus some cartoon stuff from my childhood & my kids)....
But it felt like from the start the X-men mutant thing was faction based and much more in contrast to normal non-mutant society (the whole reason Xaviers school exists) and was the the underlying plotline all along. There was tension at the start with two distinct factions taking the roles of "we can work with humans" and "we are better than humans". And then working those sides into how they interacted with society and their acceptance by non-mutants.
Civil War in the Avengers universe just feels like a manufactured plot line to sell magazines/movies to further push a series.
That's really kind of why I don't get into comics. If something doesn't stick they'll let it die for a while then re-boot again some time later under a different story arc. All of the alternate timelines and deaths/not deaths just get annoying to someone that isn't that into it.
Yeah I never read the comics either, just judging the movies by themselves. You're right that the x-men mutant vs. non mutant thing was the underlying plot the whole time, but that's kind of what I'm getting at. The fact that Marvel didn't make any effort to lay that same kind of background coming into the Civil War movie makes me question how well planned they have these movies. This just seemed more like filler than anything important.
As time goes on these movies seem more like self contained little adventures instead of progress in the same universe. Since I'm not a comic guy I don't have any idea how it fares to the comics, but the idea that at some point they'll have the Avengers group with the Guardians of the Galaxy makes me less excited, and more worried that it's going to be a giant clusterfuck based on how little build up there was going into this Civil War thing.