I raced ahead of everyone to about ep 15.
Honestly, the reason it frequently rates mentions as underrated is because it's not everyone's cup of tea. You also have to consider the time that this anime was created in (art).
I really enjoyed it so far and plan to resume it. I love the visuals (if you overlook the datedness, there's some real creativity there, especially with the shadow puppet art style) and the music, and Utena is a great character. The anime is definitely a slow starter (it has 40 episodes too...) and it takes the final ep of the student council arc to make it apparent why the arc is even relevant, but the story has finally upped the ante. I think to be able to withstand Anthy you have to look at her philosophically, which exposes the hypocrisy of Utena's own creed. The duels are metaphorical more than anything at the start as well.
I feel that I can't judge this show adequately until I get further in, because the buildup here is really obvious. I hate the filler episodes but thought the advancement of Anthy and Utena's relationship was both subtle and complex so far. I don't think it's meant to initially be easy to understand. The student council arc being like 90% reused footage and failing to engage the viewer with either good battles or engaging characterisation from the council (sans one character) for like six episodes is very valid criticism nonetheless. The latter does get better though.