I have finished the man questline for the thieves guild, done at least five quests to each major hold and finished the main one to establish bases in them. Still no trophy. Any thoughts?
This is an odd trophy. By that, I mean they don't make it very clear what you have to do to unlock it.
Luckily, it's actually pretty easy. Once you have all of the shops in the Ragged Flagon, you should reach a point where Delvin or Vex will tell you to speak with Brynjolf in the Cistern. Once you speak to him, the guild will perform a ceremony to officially grant you the title of Guild Master. Once the ceremony ends, and you're given access to the tribute chest, the trophy should unlock. If it doesn't, then it's likely going to be a bug.