We'd been expecting a lot of features to carry over from GSC, and then were unpleasantly surprised when they didn't. We went from having a vibrant 24/7 world to not.
But the biggest problem was the lack of backwards compatibility. Unless you were willing to invest in a cheat device, almost half of the Pokemon that existed at the time couldn't be caught for a couple years, and that included most of the Kanto and Johto Pokemon the fans had fallen in love with.
And when they did start showing up, they only showed up in dribbles. About fifty of the missing 184 showed up in Colosseum.
It wasn't until after FRLG and Emerald that you could catch everything on a handheld again.
"There is no overkill. There is only "Open Fire" and "I need to reload." The Seven Habits of Highly Effective Pirates-schlockmercenary