Ah Pokémon. The only series that can lather, rinse, and repeat it's formula and people will still flock to the stores in droves to by these games. I've been with this series since the beginning. I've enjoyed every Generation so far (yet to play Gen 6) by favorite to least favorite.
1. Generation 2 - Not the first Pokémon generation I've played but it is the 1st that I've owned. I feel like Crystal has aged fairly well. It's still a lot of fun to play, the soundtrack is imo the best of any Pokémon series even though you can't run and don't have the luxury of special abilities it's a good time. I love that you can explore 2 separate regions and it gave me the toughest battle I've had yet in a Pokémon game with Red atop of Mt. Silver. Nostalgia may have some influence but then again most of them do.
2. Generation 3 - I remember being one of the first to get a copy of a Gen 3 game before it was released in the U.S. I thought this game did a good job in shaking up the foundation. It's started making the series feel more "alive" if you will with the region changes and weather effects added. (Well technically Gen 2 started that with the Day & Night system). But anyway it introduced special abilities and natures which can shift the battle in your favor. It had a good roster of pokemon (added more Dragons and Dragon Pokémon are the best so extra points). It gave remakes of Red & Blue, they're not bad but are my least favorite Pokémon games I've played and I'd honestly rather play the Gen. 1 originals. But my only problems with this region are
(1.) the gameplay is too short. I got Sapphire for my 12th Birthday and I beat the game in 3 days, Emerald extended the gameplay and made it more fun but after you beat the champion there really isn't anything left to do.
(2.) TOO MUCH FUCKING WATER!! WHY IS THERE SO MUCH FUCKING WATER!! WHY ARE THERE SO MANY TENTACOOL, WINGULL, PELIPPER, & WAILMERS?!?! WHY, WHY, WHY?!?!?
3. Generation 4 - It took some time to warm up with this generation but I love it. It expanded on the more life like system that Gen 2 and 3 started, the 3D is a cool touch, another good roster of Pokémon but the flaws I find in this generation is the gameplay is almost just getting badges. Like after you deal with Team Galactic for the Final time you're just getting badges one gym after the other.
I'm a bit too lazy at the moment to go into details for the rest so
4. Generation 1
5. Generation 5