Honestly, when I think of a draft/league format to Pokemon, I think of a weekly round-robin style competition (with an eventual playoffs) rather than a straight-out tournament. Eight teams pick eight or nine pokemon each, facing off against one team each week for seven (or fourteen :p) weeks in order to be placed in brackets for a final tournament (ranking first by win/loss, then total pokemon left standing in wins, then total pokemon not KOed in losses).
Each week, a team is allowed to add one pokemon to their team, at the cost of dropping one of their current pokemon - of course, that pokemon would have to clear waivers first, going say 24 hours without being claimed by a team with higher priority (any team that claims a pokemon is sent to the bottom of the priority list). Trading is allowed on a one-to-one basis, either unlimited or also set to one per week. For playoffs, rosters are expanded to 10-11 pokemon, with the last-ranked team given first priority in choosing its first new member.
The problem with this format is that it would require a long-term investment by all participants in order to work, which might not be viable due to last-place teams choosing to quit midway through the process (even though all teams would make the finals), and that it does not reward teams for their placement in the regular season (some kind of home-field advantage would need to be devised, such as limited control over special clauses to be put into effect - most likely, home rules would have to be established before any games took place for each team). Advantages to this system include allowing opponents to metagame each other by adding on specific pokemon to counter their upcoming threat, scouting matches, or choosing to stay the course with their pokemon and grab up bargains for the postseason (at the expense of home-field advantage).
If sixteen people could be troubled to participate in the draft/league, teams could be split into two seperate leagues (Kanto/Johto, for naming purposes alone). Each league of eight would draft from a full pool of pokemon, not interacting with the other league expect perhaps for light interleague play, then combine for a playoff of eight people. This would encourage players to actively seek out victories in the regular season, as only the best four teams from each league would make the playoffs.
Yes, it's somewhat complicated. But that's what true league play is all about.
I like this idea. However, I think that the teams should start off random. Your 30 pokemon are assigned to you by a random number generator. Trading rules will apply, and you may get repeats for pokemon. Ubers and NU pokemon are illegal. Everything else is fair game in terms of the RNG. (That way, no one gets a luvdisc, and no one gets a Mewtwo)
Entirely random teams may put some players at a disadvantage, at which point they can trade in 2 pokemon for a single chance at the RNG. With 30 pokemon in your pool, this gives quite a few retries.