If I recall the Princess Lana character was 'frowned' upon because she had nothing to do with any video game at the time. (And still doesnt) I cant find any other show/game or at least a hint of her appearing in any Nintendo related thing. In the comics, I know Samus was in them and did but heads with Lana over Kevin. Still why they didnt make Samus in the show is beyond me or what I can find.
My only guess is that if it were Samus, shes a bounty hunter and a bit of a bad ass... so why would they need a "savior" from another world thus killing the the whole show... still would be nice to see it again. Like the Nintendo Avengers or something,,,