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We have exactly the same problem. We want to use challonge to live-document sports events who use some other scheems of seeding. The winner bracket can be manually rearranged. However the Losers/Hope Bracket is fixed.
However I propose a more general scheme:
Add the feature to challonge to generally define the seedings in brackets (an "external" numbering of players and matches), not as a default but as an OPTION. This would just need an intermediate absract layer and ANYTHING can be achieved.

Seeding is also a big issue for me.
However I think it has to be adressed in general to enable all kinds of neccessities.
So maybe it can be pre-organized somehow for the developers to draw their conclusions.

A) we should differ between static seeding and dynamic seeding.
- with static seeding I mean there is only the first draw: all matches and ways are set.
- "dynamic seeding": after each round, or elimination round there can/will be a new drawing. This can again depend on certain criteria, such as divide (put them on the most distant branches) the strongest players or players which are locally more close or distant. With this you can try to "enforce" stronger endgames and reduce the risk that weak players end in endgames by lucky draws. (if you want that)

B) RULES and Criteria to seed.
B1) Initial static seed and dynamic seeds
I think it will be hard or impossible to provide "all/any" criteria. Maybe it will be a start to consider each player/team with "attributes". Ideally a "real" value. I think without restricting generality we could call this "strenght". The seeding algorithm can then have the option (or multiple options) to put the most strongest players as distant as possible. And that for every round with a new draw, depending of who wins and looses. (Something like the chess ELO-number) could be a critera. Other criteras could be "vicinity" of players. You probably do not want to have players of one team fight against each other in the beginning, but allow them all/both to reach the final.

B2) double elimination. Also here modified seeds for the loosers round would be a valuable addition.

B3) The "strenght" number could change during the game. (such as the premention ELO number). even if all players at the beginning will start with the same value, the performance of the guys in the "loosers" round could "rankup" or "rankdown" the "strength" number in the winnersround. This can help to put the stronger guys on more distant branches and avoid the strong clashes in the early rounds and spare them for true finals. It also would help to equilibrate the chances in the loosers round.

I just discovered Challonge and quickly thought this was the answer to my online bracket hosting hopes. Alas the seeding options need to allow more manual customization. Our state tournament gives the host league a first round bye, and then sends loser of Games 3 and 4 to the Loser Bracket (13 teams) whereas Challonge forces loser of G2 & G3 to go. Normally that'd be fine, but so many tournaments have minor quirks like this, Challonge doesn't quite fit yet. I think if (1) you allow users to drag-and-drop seeds anywhere, and then (2) set which losing games go to the first L-bracket, that would provide the flexibility needed. I'm really disappointed we won't be able to use Challonge for our DE 13-team bracket. I really looks like a great site, but is not quite flexible enough. Keep improving. Hope to use your service in the future!

In my current situation I would like to be able to add participants and re-arrange their seeding without having to re-enter all of the names again. For example, if I have entered 10 participants and then a new entry with a high level of skill comes in, I would like to add them to the participant list with a high seed. I am just trying this out for the first time, but I was not able to manually arrange the seeding after input. (I know that I can drag names around the brackets after, but that just causes mayhem).

I would like to be able to rearrange or re-draw the bracket between say, round 1 and 2 of a 32 participant single elimination tournament, similar to what happens in the UEFA Europa League.

i agree, i dont like having to manually seed by location and try to keep the top competitors on top. to much bracket theory. this would make Challonge the best bracket system in the world.

Thanks for sharing this suggestion! We totally agree, so it's a matter of prioritizing this. We're pretty tight on resources and time, so more votes or comments here will definitely help keep this on our radar.

I went searching through all of the posts hoping to find this. This is EXACTLY what's holding most of the smash community backing from going completely to Challonge.com. I personally love Challonge, but it's seeding options are so limited.

Please Challonge, this x1000!

Any thoughts on this?