That's not to say it doesn't look good, if it was a brand new game, it'd be hard to complain. But the original has a very specific composition to its design that you're stuck comparing it to, and tossing in all the new tech and stuff messes with that. Creates areas of disconnect which changes the mood and such of scenes.
Whereas when you run it through Dolphin you're just upping the resolution and smoothing it out.
It's a small thing, but somewhat annoying none the less. I can't imagine TP would run into many of those problems though as it was already going for that kind of look. Skyward Sword might be a different story.
Though Nintendo, if you really want to draw me in, let's start talking about a Metroid Prime Trilogy HD. I don't know if I can resist buying those games yet a third time. Especially since Corruption already tries to fake all kinds of shader effects that could be done properly. And you could bring back the stuff you dumped from Trilogy's versions of 1 and 2 since we're back to gamepads.
I won't even complain if you wanted to toss in Other M. That disc can accidentally get lost somewhere.