Well, I don't really think Bayonetta pretends or tries to be smart, and I personally don't consider it a satire either, nor a pretentious game. Just my view though.
About the flaws... I'm not a fan of the monster design (what I like are the "human" characters), the cutscenes you talk about are a cheap way to save some costs (I guess) and I didn't think anything about them. Now I simply can't agree with what you say about the soundtrack. Some boss themes you can't really hear because of all the shit happening, but the rest is brilliant. Whether you like the style or not is subjective though, but while I DID think that using Fly Me to the Moon would feel wrong, pretentious or embarrasing before I played the game, I ended up liking it.
I'll repeat that I loathed the concept of Bayonetta when it was announced because all you read was "OMG SHE IS NAKED AND ONLY USES HER HAIR TO COVER HER SEXY AND BIG ASS AND TITS" and nothing about the actual game. Then came the dance videos and crotch closeup gifs... But when I decided to play it and saw what lied underneath all that I didn't care and found it pretty fun. Something similar could be said about Nier. If I had only listened to the general press saying that it was a "dmc or god of war", "there is a scantily clad hermaphrodite in the game OMG" and "it's pretentious because it tries to cover too many genres and there are walls of text in the game!!" I'm sure I would have thought it was stupid. Fortunately I had to play it because I had to review it and I could see what it really was about.
So the point is that, even though some of the most vocal fans of Bayonetta insist that it's to be taken as a satire and that everything is intented to be taken as a parody, I like to think for myself and I don't think that's true. It's not a social experiment, it's a bloody japanese videogame and that's the way they make them