OMGOMG MEGA REPLYYYY!!!....
I've never heard of Dragon Quest which means most likely the general public has never heard of Dragon Quest which means that Nintendo doesn't care to put Dragon Quest in their game... I don't suspect there are going to be almost any third party characters besides Snake, Sonic, and Mega Man.
-Strike
1. Dragon Quest is INCREDIBLY well-known in Japan. Don't understimate the importance of that. A character who is uber-famous in North America but nearly unknown in Japan has almost zero chance of making it into SSB as a 3rd party character, I'm sure, but I doubt they'd see anything bad about taking a character popular in Japan and reintroducing it to the world.
2. Just look at Fire Emblem. As an RPG series, Fire Emblem was far more obscure than Dragon Quest when Melee came out, but they included Fire Emblem characters anyway. I think Sakurai doesn't want to use SSB to advertise TOTALLY unknown 3rd party characters, but I suspect he doesn't have anything against re-introducing characters that are popular in Japan to the rest of the world.
(Yes, I know Fire Emblem is 1st party Nintendo. I still think it's worth pointing out.)
As for whether there will be more 3rd party characters, I'd be more than happy to bet you 50 bucks that there will be at least one more, or 20 bucks that there will be at least TWO more. Going by the (fairly successful) SSB Brawl publicity campaign, Nintendo is very fond of announcing characters one-by-one, and they don't use up all the best announcements at once. They spread them out, to maintain interest through the whole period between the game's initial revelation and the release of the game (possibly a whole year or more).
Dragon Quest is honestly one of the most popular and influential series in Japan (it could debated to be the most influential). It hasn't met with quite as much worldwide fandom (a lot haven't even been released outside of the US). Granted, the fact that it's not too awfully popular outside of Japan would still prevent Nintendo from adding a character from it into SSB. Plus, I dunno. I'm not sure if Square Enix would be the type of company to agree to something like that.
How about a Castlevania character? I could sort of see that being plausible.
I wouldn't write off Dragon Quest completely, but considering it's owned by "Squenix" now, you have to take into account that they might rather put forth characters from different series that are likely to cause more excitement. Like... I dunno..... Kingdom Hearts. D:
I'd kinda like to see more model variation in the characters, like how Wario had both his classic and Warioware look. It'd be cool to have Samus in a real fusion or dark suit, the return of Dr. Mario (plus maybe tennis umpire Mario, boxing referee Mario, etc.), and a Birdo skin for Yoshi (he can spit eggs instead of throwing and have a different sound set).
And I totally can't wait to play as the Wii Fit trainer. I think she's a hilariously awesome inclusion.
I would be very surprised if Samus doesn't have alternate suits like the ones you listed, although the question is whether they'll be alternate 3D models, or just textured skins. Some of the others will require complex changes to the 3D model (like maybe Birdo), so they seem less likely, though still quite possible.
Was Mega Man really that big a surprise in the first place?... 
When I saw him, I didn't say "OH MY GOD," I said "FINALLY." According to polls, he was the most-wanted 3rd party character addition in Brawl (at least among those that didn't make it in).
Bigger doesn't mean better. I'm not gonna hate on the Wii Fit Trainer, but Megaman's certainly the best new inclusion so far. If not because it's freakin' Megaman, if because Capcom finally let him have a moment in the spotlight instead of spitting all over him.
And I think everyone's happy about no more tripping.
I agree about the alternate skins, too. That would be neat, and more than feasible. Would a Protoman skin be too much to ask for... ? Probably. >.>
YESSSS...NO MORE POINTLESS RANDOM TRIPPING, THANK GOD. So many people prefer Melee, and I actually kinda preferred Brawl, but I found it impossible to argue that Brawl was better, solely because of the tripping aspect. Ugh.
Wii Fit Trainer's gonna be hilarious. I always appreciate characters who can kick butt while humiliating their opponents. Come to think of it, Pink Luigi already did that (though I'd never use HIM).
As for alternate skins, Peach had a Daisy skin in Melee, and Wario had his Warioware look in Brawl, as was mentioned, so I would not be at all surprised to see Mega Man get a Proto Man skin. It might simply be a color-swap and sunglasses, though, with Proto Man's shield on his back. And perhaps a scarf if they don't mind animating the wind-flutter. In other words, it'll probably still be Mega Man's face and body structure underneath the accessories.
Alternate Skin for Link should be his Z1 or Z2 appearance. If I owned any copy of the game, it'd be the ultimate and best choice whenever I use him. His original design was the best design :3. This isn't a case of "The original is always better!" Instead it's a case of "The original LOOKED way better" Of course they'd probably give him the original Wooden Sword as his weapon if they made a Z1 alternate costume.
Toon Link had a "classic" color option, meaning yellow band on hat, darker green, darker hair, and brown sleeves. I don't think he had the cross shield, though. Religious conflict may keep them from bringing back that part of the old design in future installments.
Anyway, if Toon Link is not in this installment, I wouldn't be surprised if they gave regular Link a classic skin with dark hair and brown sleeves, at least. Probably no more than one classic skin, though, because they probably won't want more than two where he is wearing a green tunic and hat.
With speculating on what characters will be added in, don't forget that villains are fair game. Here are my predictions...
Simon Belmont: Castlevania hasn't been represented yet, and I believe Simon is the one who could use the whip in all 8 directions, so I think he'd make a better character.
Richter Belmont: Same reasoning as Simon, except Richter's Item Crashes have more potential towards special attacks and Final Smashes.
Bowser Jr.: It's a Mario character, and small enough to work as a playable character. Has abilities from Sunshine as well as the NSMB games to draw from.
Tetra/Toon Zelda: They added Toon Link on top of regular Link, so it's not too much of a stretch to make a Tetra/Toon Zelda character with a similar tranformation mechanic as Sheik/Zelda. Also, the pirate ship can be used as a Final Smash.
The Yellow Devil appearance implies another Adventure Mode/Subspace Emissary game, so my predictions here are:
Kraid/Mother Brain: Ridley appears in Subspace Emissary, so it's likely that Kraid or Mother Brain will appear for the next one.
Medusa/Dark Pit: Kid Icarus wasn't represented all that well in S.E., so I'm going to guess that there's going to be a bit more. Also, since Uprising came out, more people will be aware of what kind of characters were in those games.
Tatenga: A real long shot, but it would be awesome to see Super Mario Land be represented in some way.
Finally, other character appearances:
Fi: Link's design in Brawl revolved more around the Twilight Princess version, so it's safe to assume this one will be his Skyward Sword incarnation. If so, Fi will no doubt make an appearance as part of Link's design or an assist trophy.
As per their "one guest character per company" policy, if a different Konami character were introduced into SSB, Snake would not be included. I'll leave it up to you to determine whether that is likely to happen.
Bowser Jr.? Well, I suspect they have an "order of succession" for Mario characters. It depends on whether they decide they need another character from the core Mario series. Super Mario has been very well-represented since SSB1, though (Pokemon has been very well-represented too, especially since Melee).
Tetra/Toon Zelda would be a great addition, though I'm not sure how likely it is. The release of WW HD will make it MORE likely, though, I'm sure. She'd probably be quite different from Zelda/Sheik, though.
Fi?... Hmmm, I would MUCH rather see Midna. Perhaps she could ride Wolf Link at some point, like during her Final Smash?... If not, then she'd undoubtedly have a Twilight portal or Twilight magic attack of some sort for her Final Smash...
EDIT: SSB4 Link clearly uses the Twilight Princess outfit, if you look at the details, but I won't be surprised if they give him a SS item. I doubt he'll have a Loftwing Final Smash, though, unless there's a SS Link preneted as a separate character (seems unlikely).
P.S. - I sorta wonder how Kirby will function. Will he continue to only imitate each character's neutral-B attack?...
If so, it makes me wonder about my prediction that Mega Man's "Metal Blade" attack will be his neutral-B. I feel as though Kirby should imitate the Mega Buster, but I really do have a feeling that Mega Man's (uncharged) Mega Buster will be an A attack. Putting it on B for Mega Man just seems like it would make it really awkward, seeing how doubly important direction is when using B attacks.
