We'll see some internal tension within the Jon/Daenerys camp but I get the impression it's way too late in the game for them to have Jon and Daenerys essentially go to war with each other with only three episodes remaining. That's a story that'd be worthy of a season-long conflict of its own. Varys has been useless in the show for years now because the writers don't actually have him do any scheming anymore.
I think it will mostly come down to Cersei vs everyone else in the end to be honest. And if it doesn't I struggle to see them setting up the final remaining conflicts in a way which allows said conflicts to be resolved effectively.
If Varys is indeed useless for the rest of the series, then why did Melisandre tell him something along the lines of: “I will leave for now but you know I will come back as I have to die in these strange lands.
Just like you, Lord Varys.”
I think he will still play a role.