So, in the end, Evol has been an increasingly aggravating ride, but a fun one, nevertheless. It didn't exactly turn out to be what I signed up for, unfortunately not in a good way, but there was still plenty of stuff to enjoy about it, even though the show's issues made the taste turn increasingly sour. As for said issues... I think all of them can traced back to one source: the writing in this show is among the worst I've ever seen. I can't believe anyone *cough*Okada*cough* got paid for this. (Oh, the individual episodes are mostly fine on their own - it's the whole picture that suffers.) I don't know if it was because they wanted to do something unique and unconventional and botched it, or simply because the head writer was incapable of handling a cast this large, but it's not like something suddenly "went wrong" somewhere, the problems were present as early as the first cour, they just got worse with time.
I'm a very character-centric viewer, so for me the biggest disappointment of the show were AMZK, who were handled in an incredibly shitty way. All four of them are characters who had good potential that got horribly wasted, all of them got shafted one way or another, and while I'm sure most people will think of Zessica at this point, for me the biggest victims here are Amata and Mikono. Amata is the textbook example of What Not To Do With Your Protagonist, and Mikono of How Not To Handle Your Heroine. Sure, destroying Zessica and devolving her into a pile of mess with her entire personality revolving exclusively about her ~love~ for some guy was horrible, and the blatant, in-your-face way they went about making her the woobie of the show for some reason didn't help at all. Kagura was ridiculously underutilized, at this point he's just a walking plot device. Still, Zessica at least received attention and push, and Kagura has enough quirks that he can still get by. Amata and Mikono, however, got very much out of focus in the second cour, which hurt all the more since they're both character types that need to be worked on, and after all the stuff that happened some insight into their thought processes or focus on them and/or their relationship would've been very important. Even individually they got the short end of the stick - they both had bursts of doing something of importance after which they sort of faded out of focus instead of staying there, and especially poor Amata got undermined almost every single time he was about to do anything. I'm very disappointed about this, because I still like these two very much, I still think they're cute and sweet, and for that matter I still prefer them to be together.
The secondary characters were just fine (Shrade, oh Shrade!), and I wouldn't have any problems with them if it wasn't partly because of giving
them development that the actual main charas got shafted. I mean, I like Andy and Mix fine, but the last two episodes shouldn't waste time focusing on their issues when there's all the main plot/chara issues to sort out! Ehh.
Characters aside, the other big issue was basically the very artificial writing that turned all characters into plot devices in some way. Again, this is not something I would've expected from the names in the staff (at least not to this extent). Foregoing natural interaction and not letting the characters have certain conversations, ignoring certain things for a long time until bringing them up was convenient, giving something a big last-minute push just because they couldn't have been assed to start developing it earlier, all in order to make the plot work... really, really bad writing that hurt the characters
and the story.
As for the plot, I never expected anything sensible so I would've been fine with anything as long as it was handled reasonably well, but-- well, the whole Apollo=dog retcon was one of the stupidest ideas I've ever seen. If it was really Okada who insisted on it she deserves a kick in the butt, and Kawamori and Yamamoto as well, for actually going along with it.
On the visual side I have few complaints, but...
While I really like the different designs for guys and girls, it would've been nice if they had been uniformized a little. It's not very jarring, but it does make me go "weh" when we see guys and girls from the side and their profiles look like they're from different shows. Add to this
ALL. THAT. REUSED. FOOTAGE. 
from Genesis, and you've got something that irritates me to no end. I was mostly okay with them reusing the Genesis soundtracks, but if you're going to reuse footage then at least get the same color palette and the same character designer you had for the previous show, for heaven's sake! I'm probably the only person who is bothered about this, but argh, so cheap, so amateurish!
Anyway, with all these complaints I still managed to enjoy the episodes, which was mostly due to the characters, and the whole thing being entertaining despite the huge flaws. And of course there's Mykage who became one of my favorite villains of all time. I latched onto him because he was pretty and reminded me of Touma (and I'm shallow), but he turned out to be very entertaining, not in the least because of the amount of fun Nakamura Yuuichi seems to be having with him. And while we're on the topic of seiyuu, a special mention goes to Fujiwara Keiji. I don't know if Fudou Zen would've worked so well with anyone else, but I'm very happy that they got Fujiwara for this role. (OK, I'm probably biased because he's one of my favorite seiyuu, but
still.)
And I've had some good fun in this subforum, well, until the overall nature of the discussion took a turn into a direction that I don't find fun at all. I suppose it was inevitable, but still, I'm not happy about it. Oh well, remember the good times, etc.