It has an unbelievable amount of filler (and some episodes are just plain bad), but I think it was the only season in which they tried to avoid being a complete commercial for the product at hand, choosing instead to tell a fun story set in a fantastical world but somewhat grounded in reality, a la Digimon.
That said... Much like the aforementioned Digimon didn't properly peak until Tamers, I think the Orange Islands season was Pokemon at its finest: raw, imaginative, wild; unafraid to experiment, and just bittersweet enough to keep you from feeling too good about the journey.