Season 1 of Pokemon was awesome. Got the story going, great characters & the battles were pretty cool (Especially when you're 6). Seasons 2 & 3 were still pretty good, but it was getting really boring. I stuck with seasons 4 & 5 simply to see how it would end. There were still some really good episodes, but they seemed few & far between. I lost interest after Series 2 came out. They brought in too many new Pokemon for me & they changed the main characters (Other the Ash).
Season 1 of Digimon was amazing. The story & characters were great. Season 2 was nowhere near as good as 1, but it still managed to get me watching every Saturday morning. It seemed right though. The original characters had grown up & so a new generation steps in, but the older guys are still there to help them along. The new characters felt really bland & the story was a bit slow for me. Season 3 was better then 2. Rika was badass & it felt like there was more depth to the characters again. Nice new twist with the cards. I only got a few episodes into season 4 & I gave up. It seemed too different to me.
Overall, I think Digimon was better quality. Pokemon had a longer run of good episodes (In my books at least) but there was a lot of boring stuff between those good episodes.