For starters, Snake has already been in Smash Bros, so they not only do not have to come up with a moveset/gameplay theme, but also can reuse, at least to some degree, his assets from Brawl and adjusted instead of created from scratch. Heck, they can even just port over his stage and the music included without having to put any effort, solving the issue of a home stage, if they wanted to keep the workload light.
Then of course you have the fact that Metal Gear is a very popular franchise, more-so than Bomberman, and Snake is very popular due to that fact and his veteran status, so the demand for him would be higher. I'm certain Snake received tons of requests during the Smash Poll, and he's often still mentioned when talking about returning fighters.
I would also guess that Konami would rather promote Metal Gear, as it is an original series (Bomberman, on the other hand was an acquisition when they bought out Hudson) and just had a new (arguable) game they would like to promote.
Finallly, I think Snake has more going for him as a fighter. I've played many Bomberman games, and his abilities always seemed more suited for an Assist Trophy than a fighter. Sure, Sakurai could make up more moves, but he always came off as a one-trick-pony to me (don't me wrong, the games are massively fun).