Yeah, they took away the way Frog spoke. Maybe it was meaningless, the way he spoke, maybe it was out of place, but it was awesome and fun, darnit. And it fit his musical theme.
As for the "bonus ending" and the "extra end boss," yes, it's made to connect the game to Chrono Cross better, which is not beneficial, and it's horrid, lazy, sloppy writing to boot.
I'd agree with Souless that CT is overrated, though. And I don't mean that as a negative about the game. As far as Squaresoft games go, it's top-notch. But there's plenty of better games out there. Although, there aren't a lot of games that do much with time travel, or necessarily do it less problematically or in a better way. I'm probably mind-blanking, but I can only think of the Legacy of Kain series.