The kind of disadvantage you're talking about it is already a structural part of the game.
Not as much as you'd think. Teams pretty much all have three or four days before the end of the postseason to set their rotations. That's why you see so many ace vs. ace matchups in the first two rounds.
Besides, so what? Just because the world isn't equal doesn't mean we have to actively legislate rules to make it more unequal. I mean, sometimes a team may lose their starting center fielder going into the playoffs, but I'd be opposed to a rule where the wildcard had to play a series without their starting center fielder just to make the regular season "count" more.
First, to be clear, MLB probably still wouldn't allow the Wild Card team to play a Division rival in the ALDS because of the "rivalry" and ratings aspect (basically, to maximize any potential Sox/Yanks, Cubs/Cards, Giants/Dodgers series). But generally I don't see how what you're saying is a change from the current system.
I don't see how it's a remedy, either, to randomly reward the second best division winner (note: NOT the one that won 97, 98, or 100 games, but the next one down that won 93-95 in a weaker division) with a weakened opponent.
Second, those A's lost their Division. Under (my) new system they would have needed to win one game at home against the 85-win 2001 Twins. Note that this is the most acutely "unfair" scenario (I can't recall such a gap between a #4 and #5) and yet I still don't have a problem with it. In NCAA March Madness No. 1 seeds like Kansas (35-3) spend a whole season dominating the league and then get beaten by No. 11 VCU (28-12). It's frustrating, it's unfair in some ways, and it's a hell of a lot of fun to watch. Yeah yeah basketball isn't baseball, but the fundamentals are the same -- sports aren't a computer game.
First, let me say that the one thing that the NCAA does have going for it is that it determines the champion on the court, in that neither team has a legislated disadvantage once the games begin. That's one of the things I object to about this new MLB proposal.
That said, you've correctly identified why the NCAA tournament, though a whole lot of fun, is really a pretty stupid way to determine the national champion. For one thing, it makes the regular season completely meaningless. I mean, completely
meaningless. If you started the season in February, no one would notice the difference. For another thing, it puts the entire idea of national champion at the mercy of six 40-minute games, meaning that a couple of weird bounces can give you an absolute dog of a national championship game with two teams that couldn't hit water if they fell out of a boat (UConn/Butler, anyone?). As much fun as the first couple of rounds may be, it generally sucks when your national championship is something like a 3 seed vs. a 5 seed. Sure, any sport can have a bad national championship game or series, but the NCAA actually gives you the possibility of having bad teams play for the national title.
If I have to watch the 85-win, not ready for prime time 2001 Twins (who drunkenly stumbled to an 85-77 record after going 30-45 in the second half) get blown out 800-3 by the Yankees again or by the Mariners because the A's randomly ran into a brilliant pitching performance by whoever the Twins ace was at the time (Brad Radke? I don't even remember, and I'm too lazy to look it up), I'm spending my early October enjoying the fall foliage instead of watching crappy baseball.