I guess it's personal preference. The concept of the "cross-over" has been around nearly as long as stories about popular characters have:
http://io9.com/5833704/a-brief-history-of-the-crossover
For Marvel specifically, it's nearly as old as the Marvel characters themselves. The shared universe that they all inhabited was one of the things that excited young readers. Marvel has crossed over with nearly everything that could be crossed over with. Remember, when comics first were created, each character lived in his own world with no other characters in sight. Once they started crossing paths is when things got interesting.
It goes back past comic books, past Frankenstein meets the Wolf Man, into literature. Heck, Disney Sea uses properties from a set of books that crossed over. Captain Nemo and the Nautilus show up in The Mysterious Island.
In video games, it's been around for many years as well, so much so that it's a standard concept. Marvel vs. Capcom. Mortal Combat vs. DC Comics.
Personally, I have no problem, specifically with Infinity where the rules are fairly set in stone (Donald Duck can't be kicking butt in the Avengers playset alongside Thor, but in the Toy Box where the
point is the mashup you can play against convention).
If they start integrating Mickey Mouse into the Marvel cinematic universe, I might raise some issues on the integrity, but in video games, nah. The mash up can be fun. IMO