Things I've noticed so far:

For enabled leagues, when teams finish on the same points a team is chosen randomly to finish above the other, I will cange this to goal difference, etc.

I haven't changed the region for the Mid Wales South League, therefore a lot of the teams from the Aberystwyth leagues that I put in this league, get moved to the Ceredigion League, this isn't a big issue for me, but the Mid Wales South League does end up with only 4 teams after one season.