Personally I think this would be a great idea and you should organise it like football.
Because there are many small legions/clans you should put battles(matches in football) on weekends. 11 players per team, 1 jedi + 2 ARCs + 8 clones for Republic and 1 sith + 2 magnaguards + 8 B1 droids for Separatists.
You make a list of teams here and win is 3 points, tie is 2, lose is 1 point. You play 4 rounds on a different map each time(or you could select every legion select it's "home" map like their own stadium)
For example you'd have:
Wins Draws Losses K/D ratio Score
41st Elite 0 0 0 0 0
212th Attack Battalion 0 0 0 0 0
501st Legion 0 0 0 0 0
152nd ARC 0 0 0 0 0
187th Legion 0 0 0 0 0
91st 0 0 0 0 0
21st 0 0 0 0 0
442nd 0 0 0 0 0
Death Watch 0 0 0 0 0
3B3 0 0 0 0 0
and so on
Then you have to organise the schedule for the whole season, which is to make sure that every team plays vs every team(don't do it twice it is too much of an organisation issue).
So the 1st BF2 League Round is for example:
41st Elite - 442nd 3 - 1
3B3 - 501st 1 - 3
Death Watch - 212th 2 - 2
91st - 21st 0 - 4
152nd - 187th 2 - 2
And then the score table looks like this:
Wins Draws Losses K/D ratio Score
41st Elite 1 0 0 2.75 3
212th Attack Battalion 0 1 0 1.5 2
501st Legion 1 0 0 2.6 3
152nd ARC 0 1 0 1.4 2
187th Legion 0 1 0 1.5 2
91st 0 0 1 0.6 1
21st 1 0 0 2.45 3
442nd 0 0 1 0.90 1
Death Watch 0 1 0 1.4 2
3B3 0 0 0 0.75 1
And so on... Until there each team has played vs everyone else and then the highest scoring ones are the Cup Champions!