I'd have to say generation 2 is my least favorite. The Gym Leaders were frustrating for me, since I was really young back when I played it and was horrible at the game ... the plot line wasn't too bad, but I really hated how the Team Rocket plot was crammed into a few spaces. In fact, the other gens did this too, except 5(wouldn't know about 6, since I haven't played it yet), but gen 2 completely crossed the border with that.
Gen 1 was the first I played. In my memory, I didn't think it was that great, since it was back in 2006 and gen 3 was already out then. When I got gen 3, I had no issues with it, the game was great, the starters were great, the Pokemon were great... just that I was confused with the new complicated mechanics, for example catching Feebas.
Generation 4 had a lot of gen 3 qualities, so I won't go deep into that..
Gen 5 was probably the best for me. Team Plasma was well spread throughout the game, the plot was well developed, and at the end of B/W, you don't even fight the Champion, you fight N. I really liked the element of surprise there.