Just registered to comment on this, a long time civ player and lurker here since CiV...
I was playing on king/continents/standard and after puppeting all of my own continent I was planning to go for science victory. Byzantium however was uncomfortably close to cultural victory on the other continent so after building a navy I was planning to puppet them too. Their first city went as planned (at which point I had 11 puppets), but with Constantinople the game did not offer the choice and just annexed the city. I was thinking that maybe it had something to do with it being their capital, but next city (Nicaea) was also auto-annexed at which point I saved and quit.
Now I tested with autosaves and re-taking Constantinople worked as usual and it asked whether I wanted to puppet/annex.
I have no mods and play with pretty much standard settings (except for raging barbs).
I was playing on king/continents/standard and after puppeting all of my own continent I was planning to go for science victory. Byzantium however was uncomfortably close to cultural victory on the other continent so after building a navy I was planning to puppet them too. Their first city went as planned (at which point I had 11 puppets), but with Constantinople the game did not offer the choice and just annexed the city. I was thinking that maybe it had something to do with it being their capital, but next city (Nicaea) was also auto-annexed at which point I saved and quit.
Now I tested with autosaves and re-taking Constantinople worked as usual and it asked whether I wanted to puppet/annex.
I have no mods and play with pretty much standard settings (except for raging barbs).