I had to choose one way, but it wouldn't be fair if I wouldn't ask the other people here. First of all, I want to present a new way of scoring system:

2x 1on1
2x 2on2
1x 3on3

Well, it sounds a bit weird, but 3on3's are usually based on luck. People just camp on both bases and sometimes there are lucky points. Also, 1on1's in JJ2 are required more skill than 3on3's. Then, each clan has to show its skills on dueling, teamplaying and the old fashioned way - 3on3's.

Also, 1on1's are much more attractive than 2on2's or 3on3's and much nicer to watch, since the duelist must do his best and shouldn't trust other people to do the job, etc...

So, each team could have it's own duelists and 2on2 teams... especially like WC3L clanwars on WC3. Indeed, the clanwars would take longer but we could start it two hours earlier and then it won't make any trouble.

That's an example of a 2x 1on1 2x 2on2 1x 3on3 clanwar:

R3ptile1_AA [ 05 : 02 ] R3ptile1_BB
R3ptile2_AA [ 05 : 03 ] R3ptile2_BB
R3ptile1_AA & R3ptile2_AA [ 05 : 04 ] R3ptile1_BB & R3ptile2_BB
R3ptile3_AA & R3ptile4_AA [ 05 : 00 ] R3ptile3_AA & R3ptile4_BB
R3ptile1_AA & R3ptile2_AA & R3ptile3_AA [ 05 : 04 ] R3ptile1_BB & R3ptile2_BB & R3ptile3_AA

Total score: AA [ 05 : 00 ] BB, a flawless victory!

Well, now vote for the best scoring system in your opinion.

Edit: If you have any questions, contact me through IRC or MSN. (Check my profile if needed)