I guess Ultimate Marvel vs. Capcom 3 is an example of a good recent crossover. Altough it came from an old crossover series from Capcom, i always enjoyed the idea.
Not only UMVC3, but other fighting crossover games are very good too. Marvel vs. Street Fighter, Capcom vs. Snk 2 (i think this one is SO cool) and Snk vs. Capcom Chaos.
I also like the "crossovers" that you can play as different characters from older versions, as it happens on Hyper Street Fighter II and Hyper Street Fighter Alpha.
About other genres of crossovers, Namco x Capcom is pretty interesting. Same goes to Professor Layton vs. Phoenix Wright.
When it comes to the recent Project x Zone games, my opinion is a bit mixed. It has a ton of characters from a lot of great games, with great visual appeal on moves. But it has too much talking, and it's a very shallow rpg, with just scenes and enemies, no shops, open maps, cities or anything like it (at least on the 1st one, i haven't played the 2nd). Very few customizations can be made, which makes this series very limited. It´s more for the eyes than the brains, even being so cool watching some of the best game heroes fighting together to save the world. A lot more could be made out of that game if he was taken seriously as a RPG.
I just think crossovers could have a bit more depth as RPG´s. The fighting ones are compentent and very well made, so why RPG´s are not?
HarvestDude™