You should base it on whats going on in your region currently, if there is a lot more of one league than the other within 100-150 mile radious of you then thats the way to go because you can tie into any regionals or tournaments for your league players.
There is no franchise fee for BCA, also BCA has no handicap system stamped in stone, you can use your own system or use a system they have put together for league operators that want to use it, or alternatively play even up if you want. They play even up at the BCA nationals. There is a player session fee for BCA players and no weekly fee to BCA, if you have a weekly fee then its set on your own and pooled for prizes and expenses.
The APA has a handicap system that must be used, and its used at the APA nationals. The APA has a set weekly fee for players on top of yearly membership fee. The APA rakes part of that weekly fee.
These 2 leagues are completely different.