So if you're so sure that OoT's time has come and gone, why does Zelda's moveset still utilize spells only obtainable in that specific game? Why shouldn't she still be able to become Sheik if she can still use Naryu's Love, Din's Fire, and Farore's Wind?
Also why are you counting Sheik out after we saw Gerudo Valley as a stage in the 3DS Version? There is no reason for Sheik to not return now.
Being in the Mario universe basically makes you a Mario character. I can accept that DK, Wario, and Yoshi do have unique ones that separate them from Mario. But you yourself called them sub-series, making them under one franchise known as Super Mario Brothers. They are, therefor, technically Mario characters. (Not sure why it matters in the long run, seeing as the only reason why this was brought up was because I suggested that adding any Mario-related character was pretty much adding a Mario character).
I'd like first say that I'm a fan of the Smash Ball-like design. I've tried it a couple of times but to no real success. The way you've ordered the characters are really great too.
I'm very much against cutting characters. If you can't add in a new Fire Emblem character, just don't add one. An Arena Ferox stage doesn't confirm an Awakening character (as both Marth and Ike are present in Awakening as well, so it very well could act as Marth / Ike's home stage despite them not originating in Awakening).
I suppose that's fair. I'd imagine Bowser Jr. behind Toad, and he makes enough sense. I still personally doubt that one will show up, but having one isn't bad by any means.
I will give you props for mentioning Fawful. Best RPG rep imo, since he isn't Mario and a third-party character.
Oh that would be cool for Lucario! It would just be weird eating a healing item and him suddenly mega devolving.
Overall your roster is pretty much perfect in many aspects.
The biggest turn off is no Ike.
Another Mario character isn't really necessary, but it's still welcome.
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On a new Mother / Earthbound character.
Porky Minch washes all of the competition out of the water (EXCEPT for Masked Man and maaaybe Kumatora, but Porky is easily the most deserving).