I can see I definitely have minority opinions about this question. Favorite is early TOS, was glad the latest movie gave them a nod. I'll admit it may be as simple as early TOS was my first exposure, but here's my rationalization. I really liked the soft, warm, rumpled look of the first ones. It made it seem as though the crew was out in uncharted space on their own where the emphasis was more on comfort and getting the job done than on military spit and polish. The pants were a little laughable but that was what made them seem futuristic to me at the time - the fact that they were so different from anything I knew. Plus I liked being able to see so much of the boot. Also liked the clear advertising of the different specialties by color. Didn't like the foolish micro-miniskirts but that's a separate issue.
I really hated TWOK uniforms. They seemed buffoonish like it was some sort of Gilbert & Sullivan operetta - "I am the Ruler of the King's Naveeey". All the buckles, straps, pockets, layers, shiny stuff, ballooned ankles - made the Federation seem too interested in trappings instead of substance. It was hard to imagine anyone actually working in them.
I did like some of the later series uniforms, very attractive to see, but their very sleekness made them seem unrealistic. Surely there would still be a few crew members who could stand to lose a few pounds or who had less than perfect figures.