I think part of the problem was that it reset Ash for the first time which, coming off the Johto anime, was a bit jarring; it threw away pretty much everything that had gone on before and offered very little to inspire me to watch it, and it never really panned out. Sure, Ash has been reset each time a new series has begun since, but he received a lot more development in DP than he did in Hoenn, BW was absolutely atrocious - far worse than Hoenn - and I don't really have an opinion on XY as of yet.
Ash's Pokemon in Hoenn weren't exactly handled any better than his Johto ones either - sure, he evolved them, but he might as well have gone through the entire season with just Pikachu and Sceptile for all the difference it made. Also, the Hoenn anime had Max, arguably the most irritating main character in the anime (not too sure about Bonnie) and the rivals for the series were especially weak...asides maybe Harley, who was a much needed breath of fresh air.
The Hoenn arc also came out at a time where I wasn't particularly interested in the franchise, and is also based off my least favourite generation, excluding BW. Subsequent rewatches have done nothing to endear me towards the series either. I'll freely admit that's probably a huge part of it: I just don't really care for the third generation as a whole.
I won't argue that May is great, but Dawn was a huge improvement, and Contests were improved in DP substantially as well. Team Rocket and Brock were both stale before Hoenn started I think. Its sandwiched between two generations I really enjoyed, which probably exaggerates its mediocrity to me, but...well, that's just how I see it.
Nah, on the contrary I'm not obsessed with her...
Advanced Generation came when majority of the fans are going through changes: teenage life, where kids at that age are starting to venture out of their childhood interests. So the reboot in the anime and game is totally understandable.
Because I honestly didn't care for it. I'd started to lose interest in Pokemon a little by that point and the anime failed the hold my attention, and even rewatching later I didn't see anything praiseworthy about it, especially not when compared to the Sinnoh seasons.