The most challenging ones the first run for me were always the ones I just didn't Realize had a pattern at first. Know the pattern on them and it becomes pretty easy.

Also, all the Sub-scenario boss's in the last chapter I ran were pretty damn easy.

The two hardest fights for me have been End of Chapter 3The Behemoth on Grandship and the Water Temples multiplying goo guy.

I edited the above spoiler.