This might have a mixed response, given my controversial feelings about certain veterans, but *if* we were to remove obvious clones/alt characters, some could be alts, some could be transformations (Zelda/Sheik, Samus/Zero Suit) but others could be replaced by (in my opinion) more interesting characters. For me, Young Link replaced with Skull Kid, and Toon Link replaced with Tetra. Add in Skyward Sword Impa, and I believe all the major Zelda titles are still represented, without any series doubling up.
Here's a roster I made, trying to come up with the "perfect" roster, including fan favorites, though there are still some odd choices I made to fit within my arbitrary rules of how each row would be set up.
Also, I should clarify, despite my feelings concerning certain veterans, I'm glad every character is returning, as it's the most ideal scenario for everyone. It's all my personal opinion, of course.
EDIT:
(some other notes I should add: I made this roster a while ago, and have made some changes since. Namely, replacing Blaze with Robotnik, and switching Inkling/Spring Man's places, adding Twintelle, removing Octoling).