I'll never fully understand the need for Bayonetta, or more third-parties, in Smash. Just because Nintendo published Bayonetta 2 doesn't mean she's a Nintendo character. She's still owned by SEGA, and Sonic has already taken the spot as our SEGA rep. She's also too recent, because Sakurai will only add third-parties who are a "huge deal", so no Shantae nor Shovel Knight either. Rayman's also not happening due to not being iconic enough (it seems that third-parties who are a "huge deal" must be from the 80's to early 90's) and Ubisoft's current treatment with Nintendo and the poor business choices they've been making. Then there's his statement back in the pre-Brawl days that he can only allow up to three third-party reps (Snake included), so no Bomberman nor Simon Belmont. The original source for this got 404'd, so all I have as its brief statement from Wikipedia, which linked said source.
Regarding the starting roster for Wii U version of Smash Bros., does this mean there will be less characters to unlock as a form of laziness or are there new unlockables taking Ness, Jigglypuff, Ganon, and Bowser Jr.'s place and can be transferred to the 3DS version? My gut is telling me that Issac may be one of them, which would explain the lack of his trophy in the 3DS version. If true, then I'll envy you for your most-wanted character making it in before mine, who will have to get in via DLC.