It would take greater organization, but instead of having one clan league, it may be better to have a number of smaller leagues, specializing in different events. I don't particularly like judo (and I was pretty busy on weekends) so I didn't participate in clan league matches that often. Had there been an alternative league for wushu or kickbox, maybe I'd have felt more compelled to participate more.
Also, instead of having one league server that everyone shares, it would probably be better if players hosted servers themselves, and invited a ref in to oversee the matches. Scheduling could be more flexible, and there'd be fewer people complaining about missing their match time due to prior matches completing early, etc.
So far as the TBFL, the fact that you could only challenge 2 spots ahead of yourself was kind of frustrating, and ultimately led to the cessation of my participation. I couldn't get a match in with the only person I could challenge (the guy one spot above me was locked out due to an existing challenge), and didn't want to take the default win, so I just stopped paying attention to it. Ultimately, it seems like more trouble than it's worth to get to the top, and could likely be replaced with random tournaments.