It's still a Nintendo IP, though, provided I'm not tripping. Game Freak does a lot, but I doubt they have the authority to make any drastic changes to the formula.
Hmm... I think they do have that authority if they want to. Obviously Nintendo could veto that, but I doubt they would unless the ideas just seemed bad.
I don't mind the discs personally, though. It's obvious that they kept it in for either tradition or stylistic reasons (it helps emphasize the Pokemon - sort of like putting a spotlight on them). I don't think the game would suffer either with or without the discs.
I do agree that it would be nice if Nintendo really shook up the series, though. I'd love to see Pokemon abilities used for more puzzles (and maybe give Pokemon a HM move slot that can't be used in battle to prevent the necessity of HM slaves). But at this point, I don't see them really doing anything with the formula until Pokemon starts losing sales... and I doubt that'll happen any time soon.