If you're talking about Star Fox Adventures, that game was fucked up by a combination of Rare taking too long and having to re-do the game for Gamecube, and the sale of Rare. The Star Fox aspect of the story probably doesn't factor in too much, as evidenced by how un-Star Fox the final game ended being too.
Dinosaur Planet was really, really far along. The problem was that it wasn't generating a huge amount of buzz at the trade show they had it at, and rather than take a chance on a new property that could flop (back on the expensive cart medium late in the N64's life, no less), orders came from above to force the Star Fox license into it. The rumor is that journalists kept mentioning to Miyamoto how Star Fox seemed like a good fit to it, and he took the suggestion to heart. (There's at least one interview where he gives something along an "oh, interesting" response to the suggestion.)
Lots of things were gutted and altered.
A quick browse on TCRF (and
the proto) will show you that. The biggest element being the almost entire removal of the dual character mechanic.
There's no way I can back this up (it was said in a private chat), but I was told by someone involved with the game that it was Nintendo's idea to lock Krystal in a, you guessed it, crystal. There's even recorded dialogue of her and Fox having more interaction after she's free that didn't make the final cut.
That game was meddled with, and was the worse for it. And it was super-jarring to have this slow, plodding, older Fox, while at the same time Melee was out with super fast, sharp, younger Fox. It made me dislike SFA even more for the plodding pace it has.
