I've just gotten the first two US DVD's today and was bummed to find that it was in "Yuki" order. The baseball episode is at the end of DVD 2 and starts off with narration by Kyon indicating that something had happened to the world (resembling leg cramps). Of course, because tMoHS I through VI was just shown, the viewer knows to what he is refering. I much preferred the baseball episode aired after tMoHS II because it left the viewer in some suspense regarding what the heck did Kyon mean and what was it that Yuki was going to reveal about being an alien in the previous episode, etc. etc.
It also bothers me that the dialogue between Kyon and Haruhi for the previews is just "lost" ... like tears in the rain...
Anyway, I'm very disappointed they chose to do it this way, but it is probably true that businesses lose less money by not overestimating the intelligence of their potential audience. If the companies producing/licensing the series found that their viewers had been confused by the airing order then it makes sense to change it for the DVD. I just wish people, in general, were a little smarter...not the first time, either.
I'm just glad I saved the fansubbed eps.