How would Yoshi cause some problems? I'm just curious as to why him in particular. As for your concern for non-attack specials, here's what I think for some already in the game.
The concern is that every character would now have a super version of their specials, leading to a new tier of powerful attacks. For most recovery based specials I would think that their "super" form would allow them to have more recovery to compensate for the overall increase in power. Yoshi doesn't have a special that helps him recover really, and thus there's a bit of a problem. In addition, I guess tether recovaries may also hurt a bit more, since the main problem with them is how to deal with edge guarders, but you would think that their range would also have to be increased for compensation's sake, but in the case of Olimar that may impossible.
Ness and Lucas' PSI Magnet - Pulls in the opponent. Because Lucas' is one-sided, he can suck people in at a farther range.
Pit's Mirror Shield - Absorbs projectiles. The amount of damage the attack had is added to the next Super Palutena's Arrow Pit launches.
While most of these explanations are fine (though I'm a bit skeptical on Fox's) these two are a bit odd. I don't see why there would be much, if any, gain by sucking in the opponent with PSI Magnet, since it seems a bit pointless, as well as conter productive. The PSI Magnet, isn't supposed to damage, unless its activated right on top of the opponent (and that's only Lucas) so when you draw in the opponent, they can simply attack you, while you're waiting for the move to end.
Next off, I am assuming that you have to use two of your special Smashes just to get Pit's netural super special to work or something? What happens if you use the neutral super special without anything in the mirror? Why should Pit have to use two super specials for something that G&W only needs one for? (And for that matter, you forgot to put in Game & Watch's down special here, which doesn't seem like it could really work in terms of sucking in physical attacks)
R.O.B.'s Robo Burner - Attacking does not interrupt recovery. However, being attacked will stop it.
Wouldn't that really screw around with his animations though, since certain attacks need his boosters to be turned off for a second.
Oh, and n88, the general idea I had for characters having switched moves was that they would be set up ahead of battles, and would be assigned to a player's name tag. (Essentially, each name would tie into the specific configuration of the character's specials.) The main problem I see in this is that it requires each name to have the capacity for remembering a changed moveset for each character, but that could be hand waved by the fact that the next Smash game would be on a console with more power. (It may take a lot of time for someone to set up their configuration though, which depends on the person.)