Complain about the rules all you want, but when you have organized, structured competitions, there is more fun to be had.
Now, on to some ideas:
I would like to see some friendly fire matches -- bring back some long-lost stratigies.
The standard 20-minute/50-point limit seems to work well.
There should almost be a rule against unsportsmanlike conduct. Some of these children just need to be spanked.
There should be a ref for each match.
Everyone should be required to record demos in case there is some questionable behavior...
Matches should be planned in advance, with the maps and teams already picked out. If a clan doesn't show up with enough members on the match night, they'll just have to duke it out 2v4 or whatever. (under reasonable circumstances or agreement of the opposing team, the match can be rescheduled, of course).
Players can't play for more than one clan.
Clans should have some basic requirements -- like a minimum of 5 people, a web page w/records, etc. Basically some kind of stable organization that's been lacking in some of the clans these days.
Minimum of 3 people on a team for the match to count.
</brainstorm>