At the beginning of Duel in the Senate Yoda enters Chancellor's office and says:
- I hear a new apprentice you have, Emperor. Or, should I call you Darth Sidious?
Later, they exchange these words:
You will not stop me. Darth Vader will become more powerful than either of us.
Faith in your new apprentice, misplaced may be, as is your faith in the dark side of the Force.
All this sounds a bit weird, looks like they are fighting over Anakin (who would control him), not because eternal enmity between Jedi and Sith. Remember, Palpatine just orchestrated killing of so many Jedi, Anakin killed younglings, yet Yoda doesn't mention anything of that. He sounds almost like Palpatine stole his new shiny toy, and he wants it back. On the other hand, Palpatine admits that Anakin would become more powerful then he is. Yet, he doesn't seem to be upset about that, he sounds glad - very strange for a Sith.