Honestly,
I think that the best way to do this would be by team name (unbreakable bond, etc)
simply because of this
If you have it organized by leader, and have any partner you want, then most of the times will be around the same, because there are some major advantages one character might have to another. tails and cream can fly, knuckles can fly, and sonic can run
so look at it this way
Route99 Act 1
sonic
tails
knuckes
cream
amy
say the level was a running level. then the times would probably be the same, because the partner system would end up like this
sonic, tails
tails, sonic
knuckles, sonic
cream, sonic
amy, sonic
now say that the level was perhaps a flying level
then the system might end up like this
sonic, tails
tails, sonic
knuckles, tails
cream, sonic
amy, tails
I cant really say who the player would choose if they were the flying type, but youg get what I'm saying
I believe the other way is better
Route99
sonic tails
sonic knuckles
cream amy
forgot this team
ok
if this was the case, it would work out much better, because the teams are set up pretty evenly. If everyone could just FLY through the level, it would make it much easier, but this obviously isn't the case. it makes it even and fair, and you can still make a decision, deciding on who the leader is, and who the partner is of the two characters
as for ok, ok is kind of like your lucky break. You simply just choose anyone combo you want.
so I dont know about you, but this looks like it will be alot more fun and challening if we have it set up this way, rather then everybody can almost fly or run at superfast speed or swim really fast underwater, etc
this way, not everyone will be able to fly, or run super fast, or swim fast underwater, and this calls for different techniques and routes to be used, making time attacking alot more fun instead of dull. besides, once you unlock the path for one team, you most likely wont be able to use the same path with another team, while as if you were doing it by leader, everyone would probably be able to take that path, at a SLIGHTLY different pace
ok, well that's my opinion. I'm a horrible organizer, so let me know if you didn't understand anything. :)