Tamers is easily my favorite series. The main three characters were interesting, they had good development, the human and Digimon relationship was handled the best in this series, especially with Takato and Guillmon, and the storyline was really engaging. There were a lot of good fights and they threw in a lot of unexpected twists in the last couple of arcs. I also love the concept of the kids merging with their Digimon partners to reach their Mega form.
Adventure 01 would be second. It had a good cast of characters, each arc flowed into the next one pretty well and it was a solid first series. It peaked with the Myotismon arc with raising the steaks much higher with going back into the real world, but the last arc did a good job with ending the series on a satisfying note.
Xros Wars, not including Young Hunters, would probably be my third. I watched through the series in a few days, but I enjoyed it. The first half had a formulaic structure, but it worked well enough to where it wasn't too repetitive and it did have some pretty good battles. Taiki, despite being a Gary Stu, was pretty likable and even though his friends didn't have any Digimon of their own, were actually useful at times. Nene, at least in the first half, was pretty interesting and Kihara was a easily the most interesting character to me, especially during the second half of the series. The second half had a better storyline, good development for Kihara and while the finale was a bit too rushed for my tastes, it was a fairly satisfying one.
Frontier would be my fourth. At first, I didn't like the idea of a Digimon series where kids didn't have Digimon partners, but I grew to like the new concept fairly quickly. The characters were pretty decent and the first half provided a pretty enjoyable storyline. Although, after Cherubimon was defeated, Takuya and Koji were usually the only characters who could do something and the Royal Knight arc was just a chore to get through. It did end up with a good finale though.
Adventure 02 would be my fifth favorite. Despite most of the characters in the main cast being rather uninteresting and the writers clearly trying to do too much with all of the different ideas they put onto their plate during the course of the series, I thought that this was a fun series. After the Digimon Emperor arc, the storyline became more interesting and it definitely had more complex villains to help make the series more enjoyable to watch. While it's kind of a mess, it's an enjoyable kind of mess for me.
Savers would be my sixth. I liked how it was trying to go for something a bit different with older characters and a government agency that handled Digimon, but I don't think I enjoyed it as much as the other series. Most of the characters were okay, except for Yoshino who was just terribly bland, but Kurata annoyed me so much and part of the ending bothered me a bit. Still, it was a decent series, so despite being low on my list, I didn't think it was that bad. It just didn't appeal to me the same way most of the other series did. I haven't seen it in years, so I might feel different about it if I saw it again.
Young Hunters is easily my least favorite part of Digimon. I dislike it so much that I still pretend that it's a separate series, as opposed to an arc for Xros Wars. It's just completely unnecessary. It's like an extra couple of chapters for a book that already had a good enough conclusion. It felt like it was thrown in at the last minute and it really shows with its pacing, a lack of a storyline beyond fighting Digimon of the week episodes and the lack of a satisfying conclusion. It was just bad and to this day, I wish that they had given Xros Wars only an extra episode to show the characters saying goodbye to their Digimon friends and then a brief epilogue to show how they turned out instead of this arc.