Main reason was, that the game was never actually modified to Conker. It has been in development for 4 years as a Zelda3 game before the idea of Conker came along and the main (Conker) sprite was never drawn. Also, changing the sword into a frying pan was impossible to do. The main Title screen and some dialogs were also done already. Changing all this to Conker style was questionable from the beginning. And there was also the numerous shocks of most players following the project (being fans of Link).
The way the game has recently developed, I can say for sure, that Conker is not happening (SePH's wishes), plus the 4 years pre-Conker development could not be undone.