I do agree with the sentiment regarding the current -3 settlement loyalty penalty is too severe.
Being a returning player from 1.1.2 playing in 1.6.1, the rebellions are a great addition to the game. I would argue though that the -3 settlement loyalty penalty from being from another culture is too much. Apart from empire factions conquering other empire towns, the AI can't hold 9/10 of towns they conquer outside of their culture. This makes certain towns to be constantly targeted by warring factions due to constant rebellion/conquer cycle.
Even I felt that having the -3 was too much, I was given an underdeveloped Rovalt in a campaign I was playing as a Battanian and the micromanagement I had to do to keep it from rebelling was crazy. My faction had an additional -1 penalty to help too.
The -3 is a challenge, but you can (easily) manage to mark it work if you have 1 or 2 kingdom policies active that gives loyalty. Recruiting a companion from the same culture and installing them as governor solves the problem pretty much immediately.