I agree.
Metroid Prime was a fantastic remake of Metroid. The new elements that were added were quite fun, but ultimately the goal was less to add new things and more to make the old stuff all work flawlessly in 3D. It was an unqualified success.
But Metroid Prime 2 can't be the same thing over again.
"Samus Aran responding to distress call. Oh no, I dropped every single one of my weapons again like a stupid moron."
Metroid Prime 2 needs to be something entirely new. Look at the innovations with Fusion - storylines, pensive Samus sequences, and a world that unfolded less through exploration and more through a linear progression.
That's what's needed for MP2. Beyond that, isn't Samus Aran a bounty hunter? Shouldn't we see her, you know: hunting some bounty? And is the only use of that incredibly cool ship really going to be land on the planet, then take off at the last second before the whole thing explodes? Why not fly that sucker from planet to planet, taking jobs and bringing in criminals? And have a plot unfold as that happens, finally leading back to, well, Metroids?
That's how Retro needs to approach the project.