We already get things like a Captain Falcon with Blood Falcon's emblem and Peach in Daisy colors, including hair and skin color change. If you think alternates would hurt characters' identity, I don't see how those things aren't doing that already. If they already give Peach's Daisy colors, outright giving her Daisy's hairstyle and dress model, which would mostly change her front bangs and some more dress details, is hardly that big of a stretch. As far as representation and moveset goes, we have a case like Ness, where he mostly isn't even using his own attacks.
Now, we haven't seen alts that actually change a characters' name, but the Wii Fit Trainer suggests that even voice isn't out of limit this time. Besides, this time we seen to get a quite few trophies modeled just for Smash again. If they're going out of their way to make new models, why not make models that can actually add to the gameplay's visual too, and not just the trophy gallery?
The Blood Falcon skin is identical to C.Falcon, so it was simply a matter of changing the emblem on the skin, with alts like that there's not much effort involved, so it's kinda like "Why not?". Peach's "Daisy" skin is just a simple recolour, but they'd have to change the voices, and as I said, it doesn't really match Daisy's personality, so just for the sake of having her there it's unnecessary.
With the WFTs, that's a completely different situation, so maybe I'm not getting my point across properly, but they're the same character, and even though it's un-needed to have both, it doesn't necessarily hurt since they both have a role to fill together.
What's irked me is that a lot of people are asking for every single character to get an alternate skin just because one or two characters where it seems applicable have got one on the off chance. Characters like Pikachu or DK wouldn't even have alternates to fall back on if everyone got one, they'd really be scraping the barrel and it just seems unnecessary personally. Homages within colourschemes are cute but we don't need Mr L-Luigi, Paper Luigi, and Mansion Luigi as alternates just for the sake of it.
I think another common request I see is to include a version of characters in their retro sprite forms, which wouldn't work for a number of reasons, and would probably need to be a separate game (or play Super Smash Flash).
I probably sound really bitter, and I'm not saying I would say no to having these kind of alternates, heck I'd probably pay for them if they were DLC, but it rubs me the wrong way when the characters look amazing as they are, and we don't need obscure references to spin-offs for the sake of it, even if it is a celebration of all things Nintendo, ya feel?