If Fox lost the rights say, in a year with the MCU still running and Marvel wanting to incorporate the X-Men immediately, I'd say no. No because I don't see how they would fit in right now. Like the OP says, doing something like SHIELD "covering up" Mutants all this time would be complicated. Looking at the timeline of the MCU with the Avengers formed, Mutants (and possibly the X-Men) should have been public by now. It just doesn't make sense for Marvel to make an X-Men movie in the MCU-- whether in the past or present when we haven't heard squat about them in any of the previous MCU films.
Now, would they work in a rebooted MCU? Absolutely. Will we see that in a year? Maybe 20.
Guardians was the better film in terms of plot/development, characters, etc. but Avengers was better in scale, hype and execution. Hard for me to choose. Avengers was monumental but pure quality is just as important.
Still don't know why people are calling it the "DC Cinematic Universe".
Anyhow, I'm pumped. You know, tbh, if they release WW in August 2016 and Justice League comes right after in 2017, they'll have had the same build-up as Avengers (3 solos, then crossover). Same build-up = $$$$$$$$$$