They took on AnH expecting it to sell 2000 BD's. That's very poor sales. The director has said that he'd be somewhat interested in making a season 2, actually! It was just an experiment for the most part.
I think it's an interesting show that's better than the bland, mass-produced moelove that's being churned out of Japan. Visually, at least. The story is still complete nonsense, but it very obviously takes itself seriously to a fault. As in, it's not meant to be seen as ``deep'' or anything - It's written in an interesting fashion that makes the most ridiculous things seem like a huge deal. A lot like how a middle schooler would see them.
The characters are interesting, too. To be honest, their dynamic reminds me a lot of Evangelion, just with Asuka being more hateful and destructive and Rei being much more expressive, Shinji being pretentious with a Madonna/whore complex, and Touji has an afro.
The rotoscoping just isn't a big thing, honestly. It's visually interesting, at least. You think "Oh this is weird" at first but you'll probably get used to it. People just like to make fun of it because it's "different". I bet if Serial Experiments Lain was released in 2013, it'd be treated exactly like AnH. But because SEL was put out at just the right moment in time, SEL is acclaimed and AnH is panned. If Aku no Hana was released at a time when moe is not the ``in'' thing it'd be regarded as a classic, another wonderful adaptation from the guy who directed Mushishi.
That's my take on it. It's a really fun show! It just makes me sad that people are going to push away anything even remotely challenging and not give it a chance.
I guess the best part is that the next episode is the last and I can finally stop trying to defend it and people can stop taking it's very existence as an affront to anime itself.