Even in George’s recuts, there is no addendum of dialogue between palps and Vader regarding Yoda. “He’s just a boy. Obi-Wan can no longer help him” is all we get in regards to Luke’s future training.
Frank Oz always held the belief that Yoda was an elegant being who never really belonged in the marsh, swampy world of Dagobah, but there’s not really an indication that he ever met Anakin, or held an organized council in the universe’s capital. Yes, he senses anger in Luke “like his father”, but he also speaks of how long he has been watching Luke, presumably then from a metaphysical context. I imagine he gauges whether or not one should be trained in the force from afar, and old Ben was the only one who had a spark of honor and purity within him. Perhaps after his initial training, Ben too wanted to bring Anakin over to Dagobah, but Yoda told him not to, or to even mention his existence. Which would then tie in to Ben taking it upon himself to do the job, then failing, proving Yoda right.
I feel Jedi and Force don’t quite go hand in hand. Perhaps the force has been around for milenia, and instead of it being a religion in itself, countless religions have spawned from it. There’s nothing really Jedi-like about Yoda. He’s simply well adversed in channeling the force’s energy. A more reasonable explanation would be that he’s simply a bastion of nature, someone who exists to guide the pendelum of balance back and forth, and calls upon the strength of others to do it. And as such, the Emperor is the negation of that purpose. ‘Jedi Master’ might have been more of an informal title, in that it’s just happenstance for Yoda to call upon the potential of Jedi Knights in order to hold balance in the universe. But he doesn’t consider himself a Jedi.
Neither The Emperor nor Yoda seek power in that regard. They need only be at the forefront of events in order to ensure that what they stand to protect is realized; The Emperor is a chaotic neutral and Yoda a Lawful Neutral. So there is much, much more at stake than percieved when Yoda finally bites it in VI. And Luke being “the last of the Jedi” is not a call to make his friends and children start swinging lightsabers as a collective, but rather a recognition he is now the only one who can combat the chaotic fist of the emperor.
So The Emperor’s claim that Luke could “destroy us” might allude to him believing that Luke is already the protector of balance, and that there is no Yoda to begin with. Otherwise there’d be more of an effort to go after and kill Yoda, which would then inevitably drop Luke right into Vader’s hands, no matter how long it took. Yoda’s deceptive appearance may also match his presence in the force; and in The Emperor’s overconfidence he never seeks Yoda out.
Maybe the ‘Jedi Order’ operated in the same divided and nomadic way prior to the turn of Civil War.