I think a big part of the challenge is not always being prepared to fight the boss (regular enemies too). I have this curse where I will have always have a stack that does not perform well against the boss. Your right, sometimes it a nuisance to switch in other monsters when you are specifically training certain monsters for whatever reason. I can be stubborn. I also play on active, you may beat the A.I. In the turn gauge but they will always choose their actions before you unless you know your just going to use Attack then mashing X will but you before them in order que.
Well no worries, I had some annoying moments in the game but I recommend you to try to go for everything, try to go for the challenges they all make you stronger. I had great time catching everyone and you get so much extra stuff to see in the game especially stuff a FF fan will appreciate. One of the few games that really opens up if you go for platinum.