Romance subplots with the Doctor work fine.
The trick is, the Doctor has to be the one who's completely flummoxed and being led around the whole time, by someone who's at least as smart if not smarter than he is.
See the undercurrent with the Doctor/Missy relationship.
See all the shenanigans with River Song.
Those were all fine, it's the subplots with the companions that get bad. Because there's a paternal quality to their relationship, and that makes companion romances with the Doctor icky.
While I'm pretty sure both River and Missy are out of the loop for good at this point, there's other characters they could bring back. Specificially, I'm thinking of the Rani. Time Lord, has mucked about multiple times with the Doctor, is possibly an ex of his to begin with, and is still out and about as far as we know. If you wanted a recurring villain/temptress to replace the role the Master's played the last few series, the Rani might be a really strong candidate, if they can get the right actress.