First: Snake...yeah.
Worst: Setting aside the obvious (Wolf, Link, and Jigglypuff), I would have to say pretty much every one that made the characters look as bland or scared as possible. Nintendo, this is your big chance to make every character full of win. You're lucky that you don't have a Dan...*remembers Tingle*...at least not one with a moveset. So please try harder to make characters like Olimar, Lucas, and Ice Climbers more of win and less of...mediocrity. Well, Lucas' displayed his personality, but seriously, he rocks. So emphasize on that rock.
After reading these I can tell some of the posters didn't realize Sonic was the only character that the fans really put in so he was added into the game last, giving him a last-minute part in the story. At least he was in the story. But seriously, this isn't the game that Sonic should be flamed for...He's seriously going to be driving in his next game...blah...