I feel like 12-3 is more efficient, because it spawns secret stage frequently than 12-5. Sure 12-5 gives better exp/money/seeds, but during my 12-5 grinding week I rarely spawn special stage, even when my raid boss is still alive.

Few days ago I switched back to 12-3 and special stage spawning regularly.

Not sure how about the others, since it's recently happening to me.