This post spoils heavily.

But first, here's a tidbit from the review @Wolf Hurricane that prompted the present post:

In all of this, I would say the only real drawback is the male lead, Kouta Otoyama, who is honestly pretty boring - Shima and the others totally steal the show, although Shima as the heroine rightly should. It’s too bad that her love interest is so bland, but it isn’t a deal-breaker, so you should be able to deal.

The above is an example of plain looking at things wrong, since Stellvia is not a romcom or 08th MS Team. Tatsuo Sato went out of his way to demonstrate the enormous patchwork of relationships and characters, each minding their own business, yet managing to save the humanity in the end. All of that is told with the focus on Shipon as a whole, not Shipon-Kouta relationship specifically, which is why Kouta is not as developed. In short, Kouta is not the "male lead", Shipon is not a "female lead", she is the lead, period.

Note that as far saving the humanity goes, Kouta is the keystone, and Shipon is the supporting character. He could've done his job with someone else in place of Shipon (for example, Ayaka). It's not, however, the story told in Stellvia.

But now, to the business.

Most of the anime choses to deal with yuri themes to disgust me unless there's some interesting twist to it, e.g. Vandred, where Barnette's growth and Jura's support of it were marvelous to see (Barnette is easily my favourite in the show). Stellvia, however, makes unusual efforts in the disgust department, thanks to Ayaka.

As I mentioned before (on Usenet), the biggest issue here is the attempted murder of a student by another student, twice. When it happened for the first time, the issue was hush-hushed and written off as a training accident, which emboldened Ayaka to do it again. A typical dynamic, isn't it? Needless to say, it was harder to smooth over for the authorities for the second time, but Ayaka's lesbian lover, and, coincidentally, her first victim, refused to testify and thus helped Ayaka to escape accountability again. Talks about the battered wife syndrome! Moreover, are we supposed to believe that, after a little bit of crying in her room over being foiled again, Ayaka will be squeaky clean thereafter? It's inconceivable!

Time after time, if yuri comes around in anime, it's accompanied by depravity, as if all creators are soft bigots. There's a very specific exemption for high-school adoration, typified by Kaorin, which they allow themselves to play straight. But otherwise you can count on it. Is such a signifier a good thing? Certainly I learned to avoid any anime which promises yuri for that reason.

STEVEN DEN BESTE adds examples.