I've been avoiding commenting on the skill system because I haven't really understood what people hate so fiercely about it. I think it's A) that you actually do have to put some thought/work into it to get good skills, rather than just slapping on the best hat and moving on, feeling good about having made a choice and B) eventually, after significantly better stuff stat-wise comes along, they feel like their effort is wasted when they switch away and lose their nice setup. And of course C) they might have no idea what they're doing and don't care.
There are two things I would change about the fusion/skill system:
1. Make equipment fuseable with more than just other equipment of the same name. It would let your old setup be useful since you would be able to transfer your old equipment skills onto the new stuff with better stats.
2. Make some UI improvements, like being able to check the skill sheet directly from the shop and fusion menus.
I'm finding the skill/fusion system kind of fun. The menu juggling can be a bit much switching back and forth between fusion and the equipment screen to see the skill sheet though.