Yes, seperating the teams from one pool to the next is the most obvious way to avoid endless rematches, and hopefully something they'll introduce in 2013, along with the elimination of the seeding games. The double elimination will be back I'd imagine, which I don't mind as I thought it was a good system.
It's a shame that the US didn't take it as seriously as the other teams. One of my friends was in the US for while it was going on and said it barely registered on the radar of most US sports fans, which is a shame.
Competative international competitions are such a unique experience that it's a shame the US fan knows little, if anything of their joys. Most seem content to continue to look at their leagues as the pinacle of their respective sports worldwide, and in many ways they are. But international competitions offer something more & different.
B-dub - your analogy of the England situation is a good one, and there's no doubt the US was lacking key players (though they had some pretty good ones on the 2009 roster) and that the extent to which the team could be "managed" was limited.
But to look at it from a different angle I think of it as a Premier League vs England national team kind of thing. The Premier League is probably the best league in the world, it's teams dominating the Champions League and teams from Europe. But when it comes to international competitions, the England team are on the whole mediocre to good.
The MLB is the best baseball league in the world, but take away the foreign talent (Dominicans, Venezuelans, Puerto Ricans etc, etc) that helps populate the league (I believe it's around 30%) and the US team just just doesn't match up to the standard of the MLB as a whole. The quality of the MLB magnifies the image of US baseball as all-powerful, in the way that the Premier League does to the England team.
Knowing a fair bit about Japanese baseball, their roster was stacked with talent. In the first game at Tokyo Dome when we saw the starting lineup on the scoreboard, it was of true "dream team" standards. It would have been interesting to see how they would have done against a US team free from the restrictions you mentioned, but I'm pretty sure they'd have stacked up pretty well.