I usually farm 12-5 until I trigger a raid boss, then either keep farming it if I have time or switch to 12-3 if I just want to quickly burn stamina. I'm running out of uses for the level 5 manyus and am have some gold issues (feeding ampies is draining my gold badly) so I don't usually run the beginner bonus stage anymore.
Not sure on how people feel between 12-5 vs 12-3, but I like the good exp ratio on 12-5 which helps make up for the 80 stam gardens. Also I think 12-5 gives more gold/seeds per stamina, the only thing I'm giving up is it's a bit harder to get all the chests.