I think an Undertale rep if picked would most likely be Sans unless Toby specifically suggested someone else, though there's obviously a lot of factors that go into that on Nintendo's end. I could see Undertale going either way though, I think its content will expanded on next game for sure but it's not impossible it's in ways other than a fighter, like just having more music or giving it a stage with a bunch of cameos, would have to see. Personally I'd like Kris the most, but it's definitely best to wait until Deltarune is over for that. It also kinda goes against the whole theme of the character lol but it is what it is.
In terms of indie reps in general, the ones that stand out to me the most as being the most likely to become playable are Sans, Shovel Knight, Shantae, The Knight or Hornet, Zagreus, and maybe Terrarian as my contrarian edgy pick. Or like, the Imposter.
I definitely have a gut feeling on Zagreus specifically but I wouldn't give any a specific edge. I'd be happy with all of them, though I would probably like Shovel Knight the most (or Umihara Kawase those games are great). I could also see the angle that if anything it might be nice to give the indie rep to a lesser known title, keeping in spirit with the medium, though obviously Nintendo isn't likely to do that.
I will say also I definitely think Shantae's importance is overstated sometimes lol. It's an old franchise, but her games have never sold that well or been that popular even up to the present day, there's tons of other indies which are way more popular and have had a lot more impact. She has a strong dedicated fanbase with a lot of requests for her, which is enough, but I see her sometimes treated as like the queen of indies which is definitely way too much.