D.N.A²
First, I apologize in advance for this rant. Second, since it's about the ending of the anime D.N.A², here's a nice big SPOILER WARNING. With that out of the way, I really didn't like the ending of D.N.A². I refer, of course, to the last three episodes released as a separate OVA to end the series.
I could have accepted a tragic ending wherein Karin chose to leave Junta behind with his memories, though even then I would argue that it was the wrong kind of ending for this series. As it is, though, not only did she leave him behind, but she robbed him of his memories and of his choice between her and Ami. This was obviously unfair to Junta, but it was also unfair to Ami— she now has to live with Junta knowing that he might have chosen Karin but was in effect forced to choose Ami. Even if there were no danger of Junta finding out what happened, Ami should still feel an incredible guilt for being with him, taking advantage of Karin's act.
It's true that the ending might make logical sense as is, but when was D.N.A² ever about logic? It was a romantic comedy, and I expected romance to triumph at the end. I may be biased since I like Karin more than Ami, but it seemed clear to me that Karin and Junta had the real romance of the series. Thus I expected that at the climax, Ami and Junta would find that their love was the love of siblings or friends and not a romantic love, as Ami's name seems to suggest. Karin would remain in the present with Junta, since she apparently had no major ties to the future.
As it was, though, the ending spoiled what was otherwise a charming little series. (As an aside, I found it to be more charming by taking the fanservice to be part of the plot and not necessarily as, well, fanservice. I don't claim that's actually the case, and there were times when the fanservice was too blatant or misplaced to ignore, but it helped.) Come to think of it, that's exactly what bothered me about X: TV (SPOILER WARNING for X: TV): Fuuma was robbed of his free will, then was saved at the end by Kamui's sacrifice, without ever having any choice in the matter. Fuuma retained his memories, though, which I suppose would be both a curse and a blessing.
There were other problems with the ending to D.N.A², and the final plot arc generally left a bad taste in my mouth, but I just couldn't stand seeing Karin shoot Junta and then disappear. I'd like to pretend I'd never seen the last three episodes, but that somehow feels like cheating to me, and I just can't do it. Oh well, another anime for the "fun, but fatally flawed" pile, I suppose.