I'm wondering if there might be some kind of timelock planned for some of the characters. As in, some characters might not be unlockable in the 3DS version until the Wii U version comes out. This is pure conjecture, of course, but I do feel like it's in the realm of plausibility, though admittedly less plausible than the whole roster being available at 3DS launch. It'd be kinda like how Event Pokemon are hidden away in the game files, mostly or completely unhinted at during normal gameplay and completely inaccessible, lying dormant until Nintendo decides to reveal them and give them the traditional marketing push with major anime tie-ins and a limited-time event. With Smash Bros., something similar could be done fairly simply - allow 3DS players to play around with the stuff that isn't completely locked away for a few months (which would probably be the vast majority of content, so suspicions aren't raised by a glaring lack of characters or stages, also to lessen any potential feelings of being ripped off when it is revealed), then just when people are starting to get comfortable with the apparent final roster, boom; new reveal trailer outta nowhere!
Of course, with each and every one of those Event Pokemon, they were uncovered and leaked to the public by hackers well before Nintendo got around to the official reveal. Given that Smash Bros. is such a popular series and how thoroughly dissected Brawl is (not to mention just how popular the modding scene is for it, such that a major Brawl mod (Project M) is gaining competitive traction to rival and possibly exceed the base game), I'd be willing to bet that any time-locked characters would be uncovered and thoroughly examined, if not before the official reveal, definitely before the Wii U release. They might be able to slip under the radar for a little while, assuming the people who will inevitably be trying to poke around in the files from day 1 fail to crack into it, but once anybody catches a whiff of content being locked away (even if they're only suspecting bog-standard cut content ala the remnants of the cut Melee characters in Brawl) and especially once Nintendo even so much as gives a wink in its general direction, efforts would be ramped up enough to guarantee complete leakage. Hell, all it would take is someone breaking in far enough to look at file names and then poking around the character files to see something like this:
MARIO.mdl
MARIO.snd
MARIO.chr
LINK.mdl
LINK.snd
LINK.chr
GENO.mdl
GENO.snd
GENO.mdl
Where, of course, Geno is our example time-locked character that hadn't so much as been hinted at prior and is clearly not unlockable in any way. While on its own, this could merely indicate a character cut during development who has remnants leftover in the release copy, which is far from uncommon and was the case for all the Melee characters cut from Brawl, it would only take somebody to hack in a way to access Geno from the character select (which would be relatively easy in the case of a character already set up to be rendered playable only after the game's been out for awhile) for the cat to be let out of the bag completely. Cue probably a good dose of drama as people either guess him to be simply time-locked or fear the worst and flip out about potential on-disk DLC.
...Okay, I was going to argue why the timelock idea seemed plausible, but in the process of writing out the post I kinda sorta talked myself into not quite buying it any more. It's not really less likely than I thought it was before, but I'm finding it more difficult to justify Nintendo either completely overlooking or choosing to do it anyway with the knowledge that the game would get broken open within months no matter what they did. I imagine the arguments for it are probably there, I'm just struggling to find them myself after that (also I'm kinda tired right now). Anybody else have something to chime in here?