First off, I want to say that the NCAA tournament is perfect as it is. I say this even though my favorite teams are Kansas (embarrassed this year) and Northwestern (has never made it). However, with the possibility of expanding to 96 teams coming closer and closer to reality, why not go whole hog and shake it up a little bit. My suggestion: limited (or no) seeding.
If the top 32 teams get a day off, how are those 32 teams determined? How about every regular season conference champ and every conference tournament champ? I don't care if it's a BCS conference or not. You win your conference, you deserve a break. If that total comes to less than 32, you can fill out the rest with a selection committee. More than 32 and you just expand the number of teams with byes (it's easier than you think).
Have 16 six-team "pods" for the first three rounds. Regional semis and finals can work the same as before. Seed the top 16 teams overall, if you'd like, to keep them apart until the last remaining moment, but otherwise, throw everyone into a hopper and draw teams randomly to determine matchups. Each of the 16 seeded teams can "host" a pod (either on own court or nearby), and each pod would also have an unseeded conference champ (i.e. 17-32) in it, but otherwise, the other four teams would be luck of the draw. We'd be talking about tough pods and easy pods, and so forth, and teams that win in the regular season and/or conference tourneys would earn a real advantage, while matchups could be crazy and fun, with good first-round matchups, two Cinderellas facing off early and/or advancing far (due to matchups). It could work.
No one watches the play-in game now because it doesn't seem like part of the tournament. It's not on the brackets. It's not on Day One. It's just there. However, take the seedings out, and every first-round game becomes important, even one between teams you've never heard of.
As it is now, you have to win six games, against presumably increasingly-better competition each round (never works like that). With the new format, you have to win six or seven games, and you could run through the gauntlet or have a relatively-easy path to the Sweet 16. Once you get to the Sweet 16, presumably only "good" teams are left, but the Cinderellas still around add to the mystique of the tourney.
I don't want to see 96 teams, but if it happens, I want to see more craziness. The best teams would still usually win, but might as well really shake this thing up.