Ooo, that's tough. I think each season has at least one strong point about it that I really enjoy. The original has my favorite animator. R ... ... well I like Sapphir, I guess. (I don't like R much.) S blows everything but Stars out of the water in terms of style. SuperS has some of the best comedy writing in the whole series (probably to make up for some pretty lackluster plotlines). And nothing matches the stakes and gravitas of Stars.
I think S is still probably my favorite. The music, the writing: the shift in tone couldn't have happened at a better time. It isn't even that the anime takes itself more seriously - some of the Professor Tomoe gags are the funniest in the season, and the ends of seasons 1 and 2 are both very serious - but rather that there is just an overall dark and serious shift, where the stakes feel more real. Usually a dark and serious shift in a light-hearted anime is out of place, but weirdly enough for this anime it really pays off. heart
Stars is a very close second though. The stakes are never higher than in Stars, and I love episode 200 to pieces, but I feel like a lot of the comedy writing disappears in Stars and that while that is stylistically appropriate, it makes the day-to-day episodes a little of a slog.
200
200
250
