Implying that these two situations are incredibly rare and will be negligible.
Seriously though, what would happen if everyone chose to play as them? Would it be fair for one/two people to not be allowed to play as the character they want?
You could match make specifically to allow only two IC's per match online, and yeah limit how many people can play as them in local FFA. Once again, it's either make sacrifices, or don't have the character at all, and let's not forget this is a 3DS only problem. I know people won't like it, but I think it's better to at least be able to play as them 1v1 than not at all.
I hate the word "fair" in this situation. Both sides will obviously think it's unfair for them; one side is missing their character altogether, and the other don't want a character that's gimped which is understandable, but let's not try and play up the sympathy card to a fan-base missing their favorite character.
I was thinking
if the IC's do become DLC, that, because they're going to have to be limited, why not make them even cheaper than usual (or even
free) for the 3DS version. That way, if you do want them, but are upset about them being limited, you'll at least be getting what you pay for (if you're even paying at all).