Not being in 3D is not the reason X-Men First Class didn't do as well at the box office. It was the first movie after 2 lousy movies, it didn't have any of the main cast from the earlier films (no, you can't count the Wolverine cameo), and the main cast of the new movie were mostly unknown.
3D accounted for less than half of the total box office receipts for most of the movies released domestically this summer. Audiences are tiring of paying more for lousy 3D conversions. It's become more of a hindrance than a benefit, and people aren't going to show up in droves if The Wolverine
tries to do the same thing.
Just make a good movie.