The RPG takes place in it's own little timeline rabbit It's within the timeline of the original timeline of MA but around twenty something years into the future, don't worry nothing Age of Apocalypse bad
http://tvtropes.org/pmwiki/pmwiki.php/Main/Revival
There are some changes though, for instance.
Wolverine still saved Silver Hawk from critical injuries that she suffered at the hands of Heracles by doing a blood transfusion. The situation actually drove both Izumi and Logan closer I love you X-23 arrived some years later and the couple took her in and adopted her
The HGO Arc still exist and sadly Emily got powers because of the experimentations put on her but the arc involving the HGO was pretty damn epic. No stupidity on either sides
Spider-Man managed to get a punch in towards Blackheart before the heroes finish him off, the guy is The Devil afterall
Scream and Deadpool, not exactly married, but live together.
Violet is still an android but more like Rei from Evangelion, with powers.
Jubilee isn't a vampire in this one but she's still awesome.
Rachelle and Ororo are married. With Rachelle working for Tony Stark he has groomed her as a prominent business woman. Even managed to go and form a company of her own. The wedding was glorious.
She-Hulk took Squirrel Girl's advice and formed a partnership. They kick butt not only as heroes but in the court room also.
On a more important note. Civil War, 616's version, and One More Day never happened!!!