One thing to keep in mind is the population, both the total population and how it is distributed between citizens/freemen/slaves. Having a decent population with a decent proportion of slaves is important as it will allow the minor the actually afford some sort of army which will be helpful.
Changing annex limit is a good idea, but keep in mind the overall setup, you may for example want it to be possible for Rome to conquer all of Magna Graecia in their initial war, which if the annex limit is 1 requires (assuming unchanged map) either splitting Magna Graecia into two countries or giving its provinces directly to Epirus. It can be worth keeping in mind that if the only province the aggressive major borders is the capital and the second province is an inland province, then they will be content to just get tribute from them.
Diplomatic situation will help, if they can find reasonably powerful allies (or allies that have powerful allies themselves thanks to cascading alliances) they tend to survive for a fair bit, if they don't they tend to get conquered. Is not easy to predict wether a minor will tend to have decent alliances or not though (although religion and culture obviously plays a very large part).
Basically that are the only thing really done in my mod with regards to minor survivability and it works reasonably well (although the annex limit is not so much changed to 1 as never updated to 2. Also it is not as if the minors survive indefinitely, they tend to get conquered eventually).