Sephiroth could always fly, that's nothing new. He was flying all over the place in FF7. In AC, as stated, Cloud is technically just jumping very long distances. Outside of Limit breaks, he seems incapable of changing his direction while airborne (that is, flying).
Masamune said:
I think what finally killed it was Hollander growing a tiny black wing, as well. As if he didn't look stupid enough already.
Agreed, I wasn't CRAZY about the wings at any point, but at least Genesis and Angeal had been born under similar circumstances to Sephiroth, so it made
some kind of sense. And Lazard was at least a total copy (looked identical) to Angeal, why Hollander got the little wing, I dunno. It actually kinda looked like Cloud's wing from Kingdom Hearts 1.
As for things fitting, Dirge of Cerberus definitely looked very out of place in FF7's world, but I can't say I saw that with Crisis Core. I thought Crisis Core had a very similar aesthetic and color palette as FF7. Most of Angeal's copy monsters were monsters from VII like the Sahagin. I'm not sure why they you think they didn't fit.