I've been waiting for a topic like this too pop up again, as I've been thinking a lot about it.
Yes, alternate costumes are needed, and I agree with just about every one of your suggestions. Dr.Mario should be a skin, Daisy a skin, classic wario... heck, even pichu would work. As an added bonus, maybe some stuff like Dr.Marios pills could be changed, really simple but cool. PLEASE sakurai, give us skins.
Oh, also, I must mention, different characters I think can be skins, as long as they are EXTREMELY closely related. Sorry, but Dark Samus could be a samus skin. Ganondorf a C.Falcon skin, though? No way, thats ridiculous.
On the other hand, though, there is one problem. Size, hit boxes, and the like. Cel Link, for example, just wouldn't work as an alternate link skin, as he is deformed, and it would really screw things up, and would take too much work for simply a skin. Not to mention, too many alterations would change the character. Changing animations beyond graphical look would change how a character played, and would make the game unbalanced.
Luckily, though, I don't think we have to worry too much about really drastic skin changes. The simple and best stuff is most likely, and I'm excited to see what we get. Liquid Snake skin? PLEASE?