The decision with Alexayn at the start is an interesting one I feel, and then again with decision with Suliji is tricky. I had two Paladins in my group, which made them harder again. The combat against Mr. Kahyn is painful for a lot of PCs - sundering isn't used commonly by enemies, and if you're running Hard mode those Wishes are just crazy powerful.
My only issue with this one is that the VC missions you can send people on seem ... odd. The only option is to send your underlings on what is basically a suicidal mission into the Aspis headquarters - if they went in the front door, they'd be facing a CR 15+ encounter straight away, realistically. My PCs obviously had issues with this, and wanted to get the local authorities to intervene - warn them that a killer was on the loose inside the building. I'd like some other options than 'suicide mission into the building or nothing', personally.