I wonder if Jay realizes at all how much easier 2P tournaments are vs 3P, just from a tournament logistics standpoint? This would be true even in an IRL tournament; I'd love to know how they'll run Nationals and Worlds.
For the sake of putting matches together, obviously this has to happen on the same day or days. Weekdays are likely a no-go; if you do "Tuesday evening," you can't reasonably start before 5:30 PM Pacific, and can't reasonably end after, say, midnight Eastern--a 4-hour block isn't going to be enough to do much.
I'm going to cautiously advocate a "Swiss-like" qualifier with a semifinal elimination round and longer finals. Format as follows:
Qualifier:
Individual three-game matches between three players. Within the match, players receive 2 pts for 1st, 1 for 2nd, 0 for 3rd; ties split all points. Points from the three games are totaled, and those scores reported to the hosts.
Match points are given as 2-1-0, again with points split for ties. Triplets are formed so as to match players who have equal numbers of points. Alas, this will have to be hand-calculated, but I know we have a few people here who are good with Google spreadsheets (and who, you know, run the place), so I wouldn't worry too much about that. This creates an ordering of any field <243 within five rounds--about 8 hours including food breaks, calculations time, etc. Sure, it's not a perfect ordering, but it's enough to create a smaller elimination field of 27. If we get >243 players, well, tack on an extra round there.
Swiss tie-breaker: sum of player positions over the 15 or 18 games played. This acknowledges the importance of position in the same way Dominion itself does, by using it as a tiebreaker. Second tie-breaker by whatever standard Swiss-style tiebreaker you wish.
Day two, three elimination rounds. Three games in the first, five in the second, seven in the finals. About 4 hours.
In fact, maybe better to play 6 Swiss rounds anyway, 3 each on a Saturday and a Sunday, then eliminations the following weekend.
Anyway, my two cents.