Eh, I don't know that Nemo is "out of place" so to speak, though I know why it's seen that way (it's shoehorned, yes, in the fact that it's an IP used as a quick fix). Would I prefer an original attraction without Nemo? Of course I would. But my bigger issue is that it's a book report/"Where's Nemo" type of attraction. They could have done better using Nemo. It could have worked. Characters aren't always a bad thing, IMO. It's how they use them that's the ultimate problem. (But I also don't think they "need" them, but they do and a good amount of people want characters; there should be a better balance/better use of them).
I'd have preferred they put Nemo in a pavilion at Animal Kingdom (if we're putting Nemo only there or Epcot) with Crush's Coaster (or a slow-moving dark ride) and the theater show, like they did with Mermaid in Tokyo DisneySea. Turtle Talk with Crush feels more out of place to me.
The fact is we're stuck with characters in Epcot. I'm just trying to look for better ways they could be used and implemented. I'd naturally prefer it to be pure but it is what it is at this point. It's why I've grudgingly accepted Rat, it's the lesser 'problem' between it and B&TB going into France.
But I'm also a fan of the Pixar Place idea. It's something I've wanted too. Similar to what Paris did with Rat/Crush/Cars(though not that attraction, LOL)/Toy Story. An area dedicated to these rides with unique homes for them. Like Fantasyland. (But I'm also with you in that I want Small World and Carousel of Progress in Epcot).
I don't mind 'bug' in the Tree of Life, I get it, but I'd also prefer something unique and original in that case. It's the attraction in your park icon. It should be something that ties the park together.
It's kind of ironic how AK, Epcot and DHS (for now; ugh) have their park icons featuring rides/attractions that tie the park together (mostly) but the MK has a restaurant, yet the other castles have an actual attraction inside. Yeah it's cool to eat in the castle but I'd prefer a walkthrough at least. Anyway ... rambling