I placed my vote for Simon Belmont. He was in some classic Nintendo games, and I think his whip and sub-weapons would make for a unique move set.
I would also think it would be cool to see Kaptain K. Rool from the Donkey Kong Country series. The Mario and Zelda series got bad guys as playable characters ... where's the love for DKC!
Yes, I feel like Simon Belmondo would be the best candidate from Konami's side. As cool as Snake was, his connection with Nintendo was paper thin, mainly influenced by Sakurai and Kojima's good relations. Simon could be a bit of a slower character like Ganondorf with the advantage of good range with his whip.
With the release of Donkey Kong 64 on the virtual console, I think King K.Rool has a pretty good shot too!