How the "Builder Base" should have been implemented...
They could have introduced the same UI... the same P vs P.
Except that instead of taking a boat to some new land, you are taken INSIDE the world of a resource that your builder is upgrading, or building.
So that you don't have to contend with dozens and dozens of builder bases, maybe just limit it to the building and upgrade of heroes.
Instead of just clicking on your AQ, and hitting "upgrade", you have to manage the world inside your AQ. As you reach certain builder hut levels inside your AQ, your AQ levels up.
You could also guide the path of your builder bases to earn special abilities of your hero.