As someone who has not played them, I'm curious. How were they a step back from Gen 2?
KaioShin has the right idea. A lot of cool stuff that gen 2 had was missing from gen 3. There was no Pokegear, way fewer time events, no multiple regions, barely anything to do in the post-game, etc. Granted, they're still main series Pokemon games, so Ruby/Sapphire/Emerald aren't bad or anything, but they just pale in comparison to Gold/Silver/Crystal. There's this fan theory out there that gen 2 were supposed the last Pokemon games released, but they were so successful that Nintendo told Game Freak to keep the series going, thus making gen 3 a bit of a rush job. It sounds somewhat plausible but who knows at this point?