Somehow Gainax managed to cram about 0.36 train-wreck into what ended up being the middle of the series. (I've decided that "train-wreck" is a unit of series-end-suckitude. 1.0 train-wreck is Evangelion and 0.0 train-wreck is something like Hana Yori Dango.) Not only were the last three episodes of the first series plotted tediously slowly, but they were boring.
It's hard for me to accept that. The first nine episodes are so good that I can't believe the same people were responsible for the latter three.
The driving point of the series is Mahoro's lifespan; at the beginning of the series she has a bit more than 13 months of lifespan left if she stops fighting the aliens she was built to fight. (This is laid out in the first five minutes of the first episode, so this is not exactly a spoiler.) She takes a job as a maid, working for the main character, Suguru.
The last four episodes play out over the period of a single day. Episode eight is about a date that Mahoro and Suguru-kun go on; and after that, episodes nine through twelve primarily feature Mahoro's duel with Ryuuga, padded with an assload of expositional flashbacks.
The outcome of this duel is virtually foregone conclusion, and only the manner in which the duel was concluded surprised me even slightly. It did not need to be spread out over three episodes; the battle itself was utterly formulaic and I finally found myself saying, "Look, just finish the fucking thing already!"
In Sailor Moon, when Sailor Moon finally has her big battle with Queen Beryl--a battle which takes some 50-odd episodes to arrive at!--it takes three episodes to contain the entire story. The battle between Mahoro and Ryuuga is not nearly that major a development and doesn't deserve that kind of attention.
...or, if it is actually that major a development, why did it seem like an afterthought?
I can understand the need for a climactic story arc; but to be honest I don't think this was the arc to use.
Ultimately the major problem with anime that is being created from popular manga series is that if the animators run out of story, they must either stall, or come up with more story on their own; and Gainax utterly sucks at endings.
This is where it all falls down: Gainax confuses Mahoromatic--a series about an android who fights mysterious alien machines--with Neon Genesis Evangelion, a series about people who fight mysterious machines of seeming alien origin with mysterious machines of human origin (I think...).
In her own way, Mahoro is seeking redemption and trying to spend her last days living a normal life. But Gainax turns the series into a bad clone of Evangelion by focusing on her role as a "battle-bot".
Mahoro's personality--well-developed up until episode 8--suddenly takes a strange turn. Her actions make some kind of sense when placed in the framework of Japanese society, but some of her motivations do not make sense. Partway through the battle we are shown a deus ex machina weapon--utterly out of the blue--and it is promptly discarded; and when we get to the end of the fight...well, it ends, but the ending is anticlimactic and dissatisfying. And nonsensical at that--because while Mahoro uses a weapon which should shorten her lifespan, at the end of the episode her lifespan has been unaffected. (Each episode ends with a text card telling us how many days Mahoro has left to live.)
Mahoromatic would have worked best as multi-season anime, but there are problems with that.
First, no one does long-run anime any more. Few titles are popular enough to justify the expense; it costs a lot of money to make anime and it must be profitable. More episodes means more money, but it also costs more.
Second, in order to maximize profits, studios try to time the anime release date to the peak of the manga's popularity, or perhaps shortly after. This is impossible to do with long-run series; while the manga may run for years, its peak popularity won't last that long.
Third, getting TV stations to commit to multi-season series is also becoming more of a challenge. Anime is easier to make these days, thanks to computer technology, and there is more competition for TV time than ever. Japan's society is very highly novelty-driven; new new new is the watchword and no one likes things which are passé. (I once told my Japanese teacher that I was watching Urusei Yatsura. She replied, "But that's so old!")
...and besides all that, in post-Bubble Economy Japan, the money is just not there for long-run anime series.
Mahoromatic suffers from having a good story and excellent characters crammed into a single-season format, too tightly; and having reached the end of the extant story, the producers of the anime substitute their own notions of an artistic ending (read "like Evangelion") rather than remain true to the spirit of the story they're telling.