I would be pretty happy if some areas made a return. The Volcano could be absolutely beautiful with the new graphics and there is a lot of new things they can do with the new Fire type Pokémon since Gen 1 (personally I would love to see the Cave level, that pne was my favourite on N64. So mysterious...).
But really, what they have to do is make the game bigger than the N64 one. Like... A crap ton. The original was very short, had a very limited number of Pokémons and just 6 maps iirc (ignoring the Mew stage). If they can improve those areas plus keep the gameplay fun and fresh with both new and returning items... The game will be great.
Oh, and if it somehow had local multiplayer of some kind and the ability to share pictures online with other player... That would be pretty neat.
Maybe it should be more free roaming, unless being on-rails works better for this kind of game.