Team Plasma in BW1, for sure. The fact that half of them were just Animal Rights Activitists that genuinely wanted the best for Pokemon put the games in this really unusual grey moral area, and for me that was so pleasantly surprising. I even found myself questioning what I was doing in-game because I thought they weren't even that bad.
Second favourites were probably Team Rocket because they were the originals. I kinda preferred them in Gen 2 when they were just trying to scrap together what little they had left, and I felt the executives were more interesting than Giovanni. Also the levels were more interesting than the ones in Gen 1, as Gen 1 was mainly just CLIMBTHISGIANTBUILDING whereas the ones in Gen 2 had some puzzle to them~