My favorite probably goes without saying. After that, Adventure has second place, because of a mix of nostalgia and a lack of any crippling flaws. 02 and Frontier was a hard call to make, because it's really a decision of which one's flaws personally irked me the most.
02 does indeed get points for the Dark Ocean and Demon--both ideas from Chiaki, the guy who was in charge of Tamers--but at the same time, neither idea got to go anywhere. Worse: Several really boring, formulaic arcs. The majority of the Kaiser stuff was good; got a little draggy at time, but it was good. But then we got another arc of the kids running around breaking Dark Towers and accomplishing not much. Then we got BlackWarGreymon, who was annoying personality-wise, which can be summed up as 'Kids try and stop him. They fail.' Then we got more Dark Tower breaking in the real world and the international arc. Etc. On top of the rather bland group of main characters--mainly Iori and Miyako, who felt kinda flat--it got dragged down. At the same time, though, what it did well--Kaiser, Ocean, Demon--was pretty damn cool.
But I have to give the third place to Frontier. It had it's major problems; no partners, the RK arc, a mixture of dragging and rushing, and four main characters becoming useless etc, but less then 02 and, again, what it did well it did very well.