Myself...well, I came into the Pokemon series in the 2nd gen (well, in that it was the first game I actually *owned*), and that still remains my favourite out of them all - sure, ever since GSC came about, there have been major improvements on it from each new gen (as there were improvements on RBY in the form of GSC), but I feel that for its time, it was my favourite gen, and the 3rd doesn't quite measure up to it as much.
Doesn't mean I didn't like them a lot though - I've played a good amount of time on the 3rd gen games alone - stuff like abilities and double battles and the 'weather' storyline in RSE and so forth, as well as FR/LG as well which although had the somewhat 'meh' Sevii Islands (IMO), was still fun. And then there was Colo and XD too, which I also liked, despite some flaws those games had - Pokemon games with somewhat dark story-lines, teenage protagonists that blow up stuff and Miror B gain ticks from me.
But yet... when playing 3rd gen games, every so often I would turn back to GSC. It just had something (or somethings) that held a higher appeal to me than some 3rd gen games, and everything just seemed so...right about it when it came out. The real-time features for one was something I was disappointed not to see in 3rd gen games - they really did seem to enhance the experience of playing the game. Being able to go back to Kanto and beat another 8 gyms is another plus, the back-tracking was fun, the game wasn't too linear either... *recalls heading east rather than west after beating Monty the ghost-type Gym Leader*.
Music-wise as well - IMO, overall 2nd gen wins out music-wise. Each gen had their highlights (1st = Route 1, Lavander Town, 3rd - heck, just look at Miror B's themes, and 4th, the rival's theme, Champion's theme...), but GSC's music seemed the most enjoyable in the end, even if it was in beeps. They fitted the places/events well, and so forth...but that's enough rambling. Maybe it's nostalgia talking but I stick to my points.
For me, gen III was one of the weaker ones for me, but I did enjoy it, and when it comes down to it - each one to his/her own - everyone's going to have different preferences when it comes to games.