Yeah, I would agree with this -- maybe mutants exist in the Marvel movieverse, sure, I am totally good with some level of that! But both the events of the X-Men films and the events of the Avengers films seem like things that would be... noticed in the other films, you know? And they don't seem to be. (Plus there's the thorny question of which X-Men films to include, given that First Class is kind of an ambiguous reboot, right?) So I would vote for them to be slightly AU from each other, personally, I think.
In the comics, the X-Men and the Avengers have always existed in this weird sort of divided neighborhood, anyway, so far as I can tell. Like, in theory they're totally the same world, and they team up and help each other out and Wolverine is on every team ever, and stuff! But in practice, they join up for big crossover events, and then each group is sort of... mysteriously absent for the other's major stuff anyway. Even when they could help out, and there's no IC reason why they wouldn't, a lot of time they're just kind of not there, presumably for the simple reason that that many characters and groups get awfully unwieldy to keep in continuity all the time.
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In the comics, the X-Men and the Avengers have always existed in this weird sort of divided neighborhood, anyway, so far as I can tell. Like, in theory they're totally the same world, and they team up and help each other out and Wolverine is on every team ever, and stuff! But in practice, they join up for big crossover events, and then each group is sort of... mysteriously absent for the other's major stuff anyway. Even when they could help out, and there's no IC reason why they wouldn't, a lot of time they're just kind of not there, presumably for the simple reason that that many characters and groups get awfully unwieldy to keep in continuity all the time.