So I’m sure almost everyone at this point has seen The Bad Batch Season 2 trailer that Disney released about a week ago. In the trailer we see Palpatine rise in his senate pod as he says “it is time for a new era”. Judging by the freeze frame of Kamino’s destruction being displayed on a screen behind him, it’s safe to assume he is referring to the clone troopers being replaced by conscripted stormtroopers. I feel like the only reason he would address this is if clone troopers began rebelling against the empire, which is exactly what the batch has done. I feel like there is a possibility we see more clone troopers (named or unnamed) join the Bad Batch’s effort to take a stand against the empire. 
Palpatine’s presence in the show also signifies how much of a threat the Batch has become to the development of the empire. So much so that clone commandos, some of the most elite clone troopers, are being sent to take them down. Prior to Palpatine physically showing up in the show, the Batch were pursued with minimal effort by the empire because they had no clue how strong the group was as a team. 
I believe that the Batch will eventually return to Coruscant for some kind of mission, which is why we end up seeing Palpatine in the same senate room. Besides this moment, however, I don’t think we’ll be seeing much of Palpatine. We may possibly see Vader in Clone Wars animation again briefly as well. The show is definitely going to heavily focus around how the Bad Batch are trying everything they can to stop the empire gathering as many allies as they can and how willing they are to help others be free from its tyranny.