Why would Atlus do that, when their entire niche is funky Japanese stuff? Considering that the entire point of the game is similar to that Final Fantasy rhythm game, there'd be no reason to replace the music, it's supposed to be all about Persona.
Elite Beat Agents on the other hand, is easier to understand. The game was localized by Nintendo, and they wanted the game to actually, y'know, sell. Bringing over a game full of J-pop songs isn't gonna resonate with a large audience, but classic western pop tunes? Much much better. There also would've been licensing fees for the couple songs in Ouendan that were not covers. Considering that we effectively got a brand new game out of it, I see it as more of a sequel than censorship. It did include new features that Ouendan 2 later incorporated, further demonstrating that fact. Yeah, Ouendan kicked a lot of ass and I wasn't a fan of EBA personally, but at least Nintendo made the attempt.