The quality of each Pokemon series varies. I would say that the franchise was at its best from the Johto League (the actual league not the season) through Diamond and Pearl. It took a huge dive with Best Wishes but is now picking back up with XY. I would rank the series in the following order:
1. Diamond and Pearl
2. Advanced Generation
3. XY
4. Original
5. Best Wishes
Here is my reasoning behind my top and bottom rankings (without giving away too many spoilers)
I ranked Diamond and Pearl the top series because while it is a slow burn (especially the first year) once it hit the gas pedal, the series gave us the best Protagonists, Rivals, Gym Leaders, Champion, Villans, Battles, vastly improved Contests ,and actual PLOT. This series highlighted two important points: How would Ash handle someone who was the complete opposite of him and that not all Pokemon were compatible with all trainers. This series also had some of the most iconic battles such as Ash vs Paul and Zoey vs Nando. The main characters of the series (Ash, Dawn, Paul, Zoey) are fully realized characters. Diamond and Pearl wasn't afraid of using plots from the past series and planting seeds in the beginning and letting them flourish towards the end. There were some negatives such as a certain ping-ponging Pokemon and a bit of a rushed league (the Pokemon League could have easily been 15 episodes) but overall the positives outweighed the negatives.
I ranked Best Wishes the worst because while it did have potential in the first 20 or so episodes, when Fukushima happened and they cancelled the first Team Plasma arc, the writers completly lost their footing and could never recover. This series had the weakest battles since the original, the weakest plot , and the companions were reduced back to sidekicks versus Dawn actually being a co-star and Brock being the support system of the group. Ash was also regressed and acted like he never been to any other region. While rivals were introduced they were squandered and completly disappeared after the Isshu League (which was the worst Pokemon League). Trip was the worst main rival Ash ever had in the series, they never even had a full battle. Also the last year of Best Wishes no one had a tangible goal, not even Ash. The idea of rotation was a good one but not used effectivly and some Pokemon suffered from it. There were good Pokemon in the series such as Scraggy, Snivy, and Oshawott but even they couldn't make up for the lackluster of the others. Also this is the first series that Ash didn't fully evolve a starter Pokemon. Best wishes can be described as a half baked cake, the idea seems delicious at first (such as a more serious Team Rocket) but is rushed and ends up not palatable.
tl;dr Diamond and Pearl is the best and Best Wishes is the worst