Technically Next Mutation was meant to tie in with the films. It even the exact same subway lair from the 2nd and 3rd films.Lotus Blossom is probably a shoe-in for player character DLC, especially as people are requesting Karai and she's basically her 87 cartoon expy.
Mona Lisa would work in this regard as well.
And while less likely, the time traveller duo, the male Landor and female Merrik, from the Red Sky seasons, were able to go toe-to-toe with the otherwise Gary-Stu-esque Carter, so Merrik may be viable candidate as well, though she and Landor are so closely tied together they'd almost have to both be included simultaneously.
If they extend to the Archie Comics which were based a good bit on the 87 cartoon, Ninjara is also a possibility.
If they consider The Next Mutation canon to the 87 cartoon, Venus De Milo may be a possibility. But considering Shredder's fate in that show would make his role here impossible, this is almost certainly not the case (And the fans probably prefer she be gone).