It's not that outrageous an idea. If you look at B&W(haven't played the sequels yet, so don't know if this is the same), they had one gym where the type the leader used depended on your starter. Or something similar...been a while since I've played it.
Either way, they pretty much made it choice of what type you wanted to fight. More relevant to the discussion, they had 3 separate types being used by the leaders of that gym. I reckon it's only a matter of time before this idea branches out and becomes something similar to this idea.
Would be really cool if they did it. Though I'm just waiting for the last gym leader to have a legendary. Could have it part of the story. You can only challenge him/her if you find, battle, and capture/defeat the opposing legendary rather than going back to the tried and true 'evil team want to steal legendary Pokemon's powers'. Puts more of an emphasis back on the gyms themselves, which have always been my favourite part of the main game to be honest.