Keep in mind my experience with the series is only with the first season of the anime and a few of the starting chapters in the manga.
The basic plot of the show is fine, it's even unique I'd say. Story is pretty solid, art style is different, characters are "meh" but I've seen worse in a generic shounen. Most of my problems are just a collection of minor gripes that culminate together. The author says "don't worry guys, this series wont last as long as other big names like Naruto and Bleach!" and then proceeds to release a chapter once every three centuries; just enough time for the series to stay relevant without falling into obscurity. His mystery box bullshit goes on for way too long, an entire season and we're left with more questions and zero answers to anything. The bones they throw us just leave us more confused.
And then there's the fucking fanbase. God almighty I haven't seen such a self-pleasuring group of fans from a series since Madoka Magica, and that's fucking saying something. Non stop threads and posts all over the internet about just how fucking good this show is, and did you even HEAR THAT FIRST OPENING?! I hate to bring up Eva, but Cruel Angel's Thesis
didn't need to be forced down people's throat to be so popular that Korean marching bands play it, it became so while still being from a relatively niche series.