I think the most important thing to figure out isn't how to draft the pokemon but rather which pokemon to have in the draft. Most importantly, whether or not to have multiple entries of the same species or not. Take the top 9 most used OUs for example. If there are more than 9 players drafting from a pool that contains only one of each of them the nine players that get them are going to have a huge advantage over other players. (Maybe not so much the guy that gets haxrachi, but I digress.) Some of those top nine are akin to having a guy like Peyton Manning on your team. They are heads, shoulders, and elbows above the next most comparable pokemon.
I think a draft with multiple but different entries from the same species could be alright. Maybe having two Scizors, but one of them has Technician the other has Swarm. Or two of the same pokemon but with different natures. Limiting them to specific movepools and EVs would be too restrictive but I think limiting them to specific natures and abilites would work alright. The only problem would be cheating as there is no way to tell the nature of a pokemon in battle afaik.
I think a draft with multiple but different entries from the same species could be alright. Maybe having two Scizors, but one of them has Technician the other has Swarm. Or two of the same pokemon but with different natures. Limiting them to specific movepools and EVs would be too restrictive but I think limiting them to specific natures and abilites would work alright. The only problem would be cheating as there is no way to tell the nature of a pokemon in battle afaik.