I haven't found non-accepted cultures to be much of a problem in the long run. Sure, it's nice to have a bunch of accepted cultures, but that won't be the factor that decides humanist vs. religious for me. Handling culture is an extra bonus on top of the religious issues.
If you can max out tolerance of heretics/heathens (or even only one, depending on where you're planning to expand) due to NIs, decisions, or your religion, I prefer humanist. You don't have to convert any provinces if you don't want to, and you'll have an easier time in the short run dealing with cultures.
If you can't max out tolerance, religious is better. Not only do you get a great CB and a large stability cost reduction, but you can speedily convert anything except the highest base tax provinces. Your ridiculously high TTF basically ends unrest as well. If you can get additional conversion bonuses from NIs, decisions, or religion, then religious is a no-brainer (and you can even convert high base tax religious centers such as Rome in a matter of months).