Digimon is better, by so many factors. First of all, an actual plot through each season. Relatable characters with real-like problems in the real world that the bring over into the digital world. A lot more emotion and mature themes than Pokemon which is the same procedural joke over and over. Digimon can actually be watched by adults without groaning, especially Season 3 and 4.
Season 4, Frontiers was my favourite season, I know an unlikely choice but it had the best storytelling and was the most adult. Using flash-forwards and flashbacks, time travel, tormented family drama, Digimons getting fucked up evolutions and almost killing the kids, it was the most emotional and inspirational season for me. "Home Again, Takuya Returns" was my favourite episode.
I still have an action figure from the 4th season (2002), even after being a medical student!
http://img408.imageshack.us/img408/7622/digimonactionfiguredesk.jpg