Ehh...
Ice Climbers are considered one of those retro characters... and to be honest, I feel like if those 3DS limitations hadn't been a thing, and the team had more time, they probably would have been in the game. (They had them working for the Wii U if I may add.. it's things like this that make me wish the 3DS version was never devised. A portable smash is a cool concept... but it ultimately hindered the main title's development... I can only imagine what the Wii U version would have been like if that dev time wasn't spent on the 3DS version... ).. Considering this installment is all about the history, they would still fit, regardless of their standings in the market.
As for the Mother series, it may have been a "worst-selling franchise", but that was mostly due to it going unnoticed, and people not realizing just how much of a classic it was. Ironically, Smash is probably one of the main things that brought the series up front, and made people curious... and made people realize it was a cult classic. In a way, the mother series "mirrors" the Shantae series in a way... the only difference here being the Mother series got a bit more lucky...
The same thing could happen for Shantae. She often goes unnoticed herself unfortunately, and many people again, don't know a classic when they see one. If Shantae had gotten into Smash bros a few gens ago, she probably would have been MUCH more successful, and more renowned in the industry than she currently is, despite her already growing fanbase now...
I wouldn't even dare to try to pull that relevance card, as that same card is often thrown at the Shantae campaign constantly...