Going from a puppet empire to an annexed empire, especially since they fixed the courthouse bug, just screams Autocracy.
Lately I'm been going Liberty, Honor, Autocracy and Commerce. Once I get the courthouse policy I go on a mad annexing spree. I'll buy the courthouses if I can afford to, but usually just let the city built it if it's 3 turns or less.
One other good reason to go on an annexing spree is I usually take Pagodas. So I can gain an instant +2 happiness, +2 culture and +2 faith in every newly annexed city as long as I have the faith saved up to spend on it.
Commerce + Autocracy = cheap unit purchases. Even cheaper if you built or captured Big Ben.