Let's do the usual round-up of the good, the bad, and the in-between.
As usual, getting this out of the way first.
♦ I grow weary of series where absolutely everyone winds up paired up (with someone of the opposite sex, of course) in the end. In this case, it's especially grating at times because Takaya piled on so much yaoi fanservice stuff early on (and even somewhat later), then turned around and had everyone hook up in approved heterosexual relationships anyway. But you can bet I won't be talking about this much, because 99.9% of the people who complain about it are not heterosexism-conscious queers but whiny fangirls who hate the girls for getting in the way of their yaoi.
♦ The ending was somewhat anticlimactic. Of course, there were almost two volumes of epilogue, which didn't help with that, but still: it felt a little like Takaya had built the ending up and up and then realized she had no idea what she was actually going to do. It wasn't terrible, though, and anticlimactic or not, I still found a lot of the conversations that made up the climax to be really moving.
♦ Takaya could be more than a little self-indulgent. For the most part, I don't mind; what she indulged was mostly what I wanted to see indulged, too (I recall being pained that we would never find out why Kyoko said "I won't forgive you" to Kyo, although I could guess at that point, only to be shortly rewarded with a flashback of her thought process). But at times, it got over the top (note to Takaya: not all of your favorite pairings were good ideas. Really). I can see why other people would be turned off entirely by it.
♦ I was way too lazy about reading it. It took me almost nine months to get through the whole series. So now I barely remember the early volumes. Whoops?
This will get more tl;dr, unsurprisingly.
♦ The fact is, someone could have written an entire manga about the character development that would have been truly needed for what Akito went through. She had some fascinating moments towards the end, and I found myself quite intrigued by some of her premise, but she suffered from being the distant villain for too long. I don't begrudge the series for focusing on Tohru, as I loved her, but to really get the development she needed to make her arc work, Akito should have had more focus early on. But that wouldn't have worked, either. Takaya kind of wrote herself into a corner there. It's too bad I have no desire to write fix-it fanfic, although I guess someone could prompt me to at some point (right now my only real fanfic idea is Momiji deciding that he'd like to continue to wear girls' clothing on occasion as an adult because he aspires to be as cute as Tohru). Still, there were parts that I liked. I loved that even at the end, her relationship with Shigure was kind of messed-up, and that she still had awkward temper issues. More on that later.
♦ The way Yuki's feelings for Tohru were handled. I didn't go into the rage that much of fandom did over this, actually, because for the most part I thought they were handled decently. As Kakeru pointed out, the mother thing wasn't really the issue; lots of guys marry women like their mothers, after all. I liked Yuki's realization that his relationship with Tohru was based on his need to be taken care of rather than mutual companionship, and knew that he was mature enough to see that he could do better for both Tohru and himself. But I wish Takaya hadn't stressed the mother issue so much; that made it a little too neat and easy. I also wish it had happened earlier, so there could have been more time to develop Yuki/Machi. More on that later.
I am a little ashamed to admit that I found there to be so much of it.
♦ Favorite characters: Tohru, Momiji, Rin, Machi, with a side order of interest in Akito-as-she-could-have-been.
♦ Favorite pairings: let it be said I loved most of the canon pairings and have trouble deciding on favorites (with the exception of Shishou/Hana, of course, and a meh on Ayame/Mine and Ritsu/Mitsuru and probably a few others I've forgotten). But let's see: Haru/Rin because the gender reversal stuff was pretty cool and Rin is sex on legs (whyyyy are they supposed to be the younger ones? Augh), Yuki/Machi despite the pacing issues because they were just so adorable and good for each other, Kyoko/Katsuya because they were perfect for each other and that whole arc made me bawww. Kyou/Tohru seesawed back and forth between making me fall in love with it and just being a part of the story that I enjoyed. My favorite part about it, I think, is the way it was presented as both of them being freaks together, not just Tohru saving Kyou from his monstrousness. Speaking of which...
♦ Tohru. I know the perky, kind, messianic-archetype heroine is a staple of shoujo and indeed of a lot of anime and manga, but Tohru makes it work so well. Takaya shows us how she fights every step of the way to be the person she wants to be--she isn't just naturally a perfect lovable wonder who is cruelly outcast for no reason. She's a strange, insecure, ditzy girl who is in her own way as much of a freak as the people she befriends. She clings to the past and devalues herself until it genuinely upsets those around her instead of just serving as an endearing not-flaw. But she works hard to be the sort of person everyone who gets to know her loves, the sort of person he mother would have been proud of, and it shows through every step of the story. I understand why people wouldn't like her--the perky messianic heroine does get old after a while, and not everyone is up for such a straight playthrough of the trope. Okay. But I will need to stay clear of anyone who calls her a Mary Sue lest I attempt to reach through my computer screen and punch them.
♦ I've already talked about why I love Haru/Rin before, but it bears saying again. They are crazy and messed-up and still perfect and hot.
♦ Machi is a weird and wonderful space case and I love that she got Yuki in the end.
♦ Oh, screw it. It may have been cheesy and trite as hell, but all the characters' stories were so heartfelt that I sympathized with every one of them. I love when an author can make me do that, and Takaya did it so well, somehow. Everyone had a reason for acting as they did, and learning the reasons made me feel for them. Maybe it's not that simple in real life, but it's nice when a story can make you believe it could be, for a little while.
♦ I loved that the ending acknowledged that despite all the sweetness and light, it would take years and years for everyone to get better. I love that Rin was still upset and angry and most of the Sohma NPCs were still struggling with the changes.
♦ I know some people didn't like the flashbacks, but I loved Katsuya and Kyoko's relationship, and getting to read that arc made me very happy. In general, flashbacks might be cheap plot devices, but every time one cropped up in this series, I ate it up. Actually, I ate up cheap plot devices in general in this series.
♦ I have thought before that no matter what an author's skill, if they dislike their characters, I will feel dirty reading the book, and if they love their characters, I will enjoy it. It's very, very clear that Takaya loved her characters, and that made Fruits Basket a very enjoyable read.