I don't think that the Shinespark tricks required in AM2R are more difficult than those required in Fusion and Zero Mission for 100%, fwiw. And though I like the extension of Metroid 1 that Zero Mission offers, I will say that I would have been livid if it were inserted into Metroid 1 proper instead of being placed after, if that makes sense.
As for Metroid Prime: Though you may not be comfortable with first-person movement as much, the reason it's so well-regarded is because it absolutely has the best platforming physics (e.g. requiring jumping) of any first-person shooter ever. Consider the platforming sections in Turok: Dinosaur Hunter for N64 or some other game, and it's a whole new world. In 2002, the graphics were also out-of-this-world good, which doesn't hurt at all (seeing accurate reflections, including Samus' own face in the right lighting, was a new thing back then). The Morph Ball sections are about as good as you can possibly get in 3D as well.
Not saying you have to like it or anything (Newt doesn't particularly care for them either, and he loves 2D platformers), but I'll say that there will probably never be a _better_ conversion of the franchise to 3D than the first Prime game.