I dont think there should be an order of the gyms... We are all on at different times and it is difficult enough to be on at the same time as a gym leader already without having an order for the gym leaders.
I think all challengers should be able to battle the gym leaders in any order that they want or the order they see the gym leaders online. If they lose because that particular gym leader is stronger, they can always battle at a later date.
Edit: Also, we would have to have a tournament to decide the order and in that tournament, there is obviously going to be some undesireable type match-ups in the tournament at one point... i.e. dark vs fighting, electric vs water, fire vs grass rock vs ice etc. etc.