I've watched it both ways and I prefer it in chronological order because stuffs are easier to understand that way.
The best part about aired order is, in the episode before they're in some sort of trouble. But in the next episode they're completely somewhere else and that leaves you going "wait..why are they in the desert? shouldn't they be dying in the park?"
Well because of everyone discussing the show here, I decided to download it and see how it is.
I will say that the original aired order is something unique to the series, but I became irritated at the fact over the character's true backgrounds were not revealed in the earlier episodes in the original aired order.
However watching the show in actual chronological order removes the "uniqueness" of the show.
It's just the Metroid series remade for the Xbox crowd.
However Samus Aran is now some unknown low ranking military personal.
Also the space pirates worship some giant doomsday hula hoop machine.
Karakuri Circus, Mx0, Red River, Rosario+Vampire, One Piece
Nintendo Wii Friend's number
Initially, I watched the show Chronological.
However the aired order does give the show a more romantic impression.
I watched both >.<
Back to topic, I recently rewatched the series in chronological order to see how it was, and once you do it, you realize that the last aired episode feels like the last episode of the series. (Of course it does, it was the last episode.) Things are looking bright, everything feels nice and happy . . . and then, the next chronological episode feels out of place. It kind of ignores the last two, three minutes of the episode before it, concerning Kyon and Haruhi's "date." However, the last chronological episode does still feel like a good ending episode (though not as good as the last aired episode). I guess the creators did it that way on purpose.
All glory to Haruhi! The one and true God!