*Sigh* people are still using the "Man of Steel outgrossed every Phase One film but The Avengers!" card?
And that's an unlikely achievement? It's for crying out loud. Barely anyone cared for Iron Man, Cap or Thor from 2008-2011. In fact, you're still saying MoS underperformed since it only grossed 60-80 million more than Iron Man 1 & 2.
RDJ's playing 60's/pre-Demon In The Bottle Tony. I never disliked his personality prior to the films (and Bendis incorporating RDJ to the character), but I didn't really invest in him either. I love what RDJ's done with Stark. I don't mind when he has alcoholic breakdowns or acts like an arrogant pr*ck these days. He's only added to the character.
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.