Personally, I would want a more open world style game. Where you can start anywhere, go to the gyms in any order, etc. No dancing men railroading and such.

The gyms could be justified by making gym leader teams based on how many badges you already have. What I'm not sure about is if doing this how you deal with trainers/wild pokemon. I guess you could have most wild pokemon running around at level 5-10, with higher level pokemon being rare. (This then makes repel very useful for training, as you just get to ignore lower level pokemon), but I can't think of any logical way to avoid having trainers that are way higher or way lower than you without the railroad pokemon usually implements.

Either way, I would also want the Pokemon League/Champion to be like, the real end game. Not "You need to finish this to open up the other half of the map and do stuff". All that other stuff should be available from the get go, beating the Champion should be taking down a team of optimized level 100s, and be a real challenge even to longtime players. It just makes no sense to me that you beat the Elite 4/Champion, then you unlock new areas where the wild pokemon and trainers (including friggin toddlers) are all higher level than the pokemon league.