Per city culture + science increase is definitely too high. Annexing over puppeting is very rarely a good idea. I'll only annex 1 in 10 or so cities for supply cap, sometimes less. Whenever I experiment and just annex everything that's in a good position (something I could see myself settling) the game falls apart as I can't produce nearly enough culture/science to make up for the massively increased costs.
If the AI is/was snowballing too hard with lower science/culture penalties per city then maybe a different solution is needed, but it makes the annex vs puppet decision and settling choices stupidly easy as a player and leads to more boring games. It never seems to make sense to settle with Pioneers for example, or even Conquistadors.
EDIT:
Also have you considered adding +1

per city to authority when Barbarians are disabled?