Hardest is probably the wrong word so I'll go with "most effort". For me it would have to be a perfecting a few of the Abyss stages. I had a lot of good, strong characters geared up but none (at the time) were gun users. Coupled with the score, other weapons and, worst of all, crystal requirements it took a fair bit of shuffling around characters, gear, testing and retesting in order to find a setup that let me perfect everything in order to complete all the floors.

I think I came in at a really good time (Maria's LC) and was able to build a strong core of supports and tanks fairly quickly so I didn't really struggle to complete content until the Abyss came along and shone that light on my strong but shallow team compositions. I've since expanded a bit more but I still don't have a geared gun user lol