Team Galactic was extremely lackluster in hindsight, of course they were an improvement from the likes of Rocket/Magma/Aqua but they hold no depth in their operations nor did they have any true consequence upon the anime as a whole... The Lake Guardian aspect with Ash, Dawn, and Brock really amounted to a very disappointing result and the only real action involved came from a brief capturing of Dialga and Palkia.
It was a decent amount of build up for a rudimentary finale, imo.
Team Flare, obviously. Even though they only started to appear after Ash's 7th Gym Badge, the writers handled them extremely well. My only minor complaint is we didn't get AZ, but who cares now. TF's plot is the best by miles now, and wonder how TS/Aether Foundation will top this.
Team Galactic by far. They established themselves as a legitimate threat early on and had great buildup throughout three seasons. They were an ever looming threat and you felt it because you knew what they were capable of. Team Flare didn't show up until near the end and all they did was destroy one city and capture Ash for like two minutes...Galactic also had a much better and more interesting payoff. Flare was very dull and flawed in comparison. I mean Flare is still a little better than all the others, just not Galactic. The fact that Galactic got away with a lot of crap before their ultimate defeat also really seals the deal for them as the better team.
I liked the Flare arc. It took a damn long while to reach a climax, but it paid off for the most part. Stunning animation, Ash at his most competent, a climax involving every gym leader chipping in, and I have preference for the evil teams Team Rocket get to be a legitimate rival for rather than the outclassed comic relief.
That said Flare technically isn't finished yet (and given the plot for the Sun/Moon games, might not even be finished by XY).