well the thing with utena is most people who love it saw it a LONG time ago so you really have to factor in the nostalgia element. i don't know if i'd like as much today than when i first saw it. back like 7-8 years ago, it knocked my socks off. now, probably not quite so much.
first arc is typical shoujou, second arc is (basically) filler, after that though, things really get interesting.
if you love wading through masturbatory symbolism, this is a series for you. i especially liked a lot of the fitzgerald-esque color symbolism.
up until i saw utena, most of the anime i had really seen was typical 90s cyber-punk stuff, so yeah, it totally changed my opinion of anime. in fact, it's what i credit changing me from a casual to a serious fan.