Is that really the same thing though? People knew that BAYONETTA was a Sega game..IE a Sega game made by PG who made their debut under the Sega banner. Also a lot of the references were subtle.
The diference here is that Bayonetta is wearing Nintendo costumes et etc and its way too much in you're face as compared to the Sega game where the references were more clever and didn't detract from the game.
Yeah, people know it's a SEGA game hopefully (although I have seen many people assume it's now a Nintendo franchise), but I'm sure there are fans out there who thought the references to SEGA were a bit much too (other than the "Eggman" reference, I was okay with all of the references), as there are sadly people who don't like SEGA (experienced a few in my time).
If Nintendo's costumes become mandatory in the story or are required to get other weapons in the game, then I'll have a problem with it, but as far as I know, they've only shown them on Nintendo Direct to hopefully move more units for the more mature Nintendo fans out there (no idea how many there are, probably not a lot).
All in all, I am happy the game exists and the other stuff is just extra.
I can confirm that Bayonetta 2 still has SEGA references in it.
I saw the Biplane cutscene in one of the trailers and thought of the Tornado.