I'm surprised at alot of hate for the B/W saga. Me, personally, the D/P series nearly killed it for me. The animation, the annoying/confusing dialogue, TR was just as annoying, they were unwatchable. The Ash/Paul rivalry grated my nerves cuz Ash was always trying to be his friend one minute and beat him the next, Dawn/Piplup and the Pokemon Contests and her rivals were just....annoying. The Black/White series actually restored my faith in the anime.
The Kanto/Hoenn saga will always be my favorites. With Kanto, its just nostalgia, and the series was both funny and enjoyable to watch as a whole. Even though its old-school anime-style compared to today, I always find myself going back to my DVD Box sets to watch them over and over. Matter of fact, I'll be watching them over again seeing as how this year marks 15 years since the anime hit the US i believe.
The Hoenn Saga i actually liked. The animation was more evolved but the humor and the action and the battles were even better back then. May was a great asset to me, can't say the same for Max he was annoying at times for me.
Johto was mostly filler and a lil boring to me seeing as how they only had 100 new Pokemon around that time and they'd introduced one only once an episode then later every other episode. Most episodes contained the same Pokemon from Kanto and the series itself was really slow-paced. But funny thing I still would watch the Johto saga over the D/P saga anyday.
So right now, Pokemon stands as my favorite, mainly cuz its the only anime I watch right now