I've been saying the same thing as you, no reason both can't exist. The problem is the location in a lot of instances, but also the execution. As you said, Nemo fits the theme but it's a bad integration of the IP (I think poor use and the idea of an "IP mandate" is why some resent IP so much, not that quality can't exist, we just don't often get it). Same as UP into Flights of Wonder. It works and fits, but they just wanted to shoehorn the characters in place. It felt like they had a totally IP free show in mind and then made it Disney Junior with birds. But it's not the worst in the world, they just could have done a lot better.
I mean, Inside Out and Incredibles get re-themed attractions on a pier. It's sad.
You've been saying what I've been trying to say for the longest. IP doesn't "have to be" the end of the world, but the main problem is execution. It's often lazy and shoehorned when it doesn't have to be.
I'm all for Rat in France. I know some aren't but I thought it was the perfect fit. I'm also all for Mary and Coco. We all want non IP rides as the first choice, but it doesn't have to be 'sky is falling'. The problem remains in the execution. As you said, if Frozen were in Fantasyland it wouldn't get nearly as knocked.
EDIT: It's why I've been pushing Big Hero 6, Inside Out, WALL-E, as IP's that could easily work in Future World, paying homage to the past while offering a new experience tied to an IP (I've even come around to using bugs in The Land). We'll see how they handle Guardians. Maybe they've learned their lesson? But they still try to be lazy so I can't trust them 100%, lol.