"Which might explain why Prime 1 is the most like the 2d Metroids while Prime 2 and 3 started to differ more."
That's a good thing, cuz I can't stand Nintendo's habit of repeating Ocarina of Time/Link to the Past Fire/Water/Earth/Forest/Slime temple design in every "canon" adventure they crap out.
"As for Corruption's linearity, I can't defend it."
I have an explanation. Too many people "got lost" playing Prime 2, and some whiners were pretty vocal about alleged backtracking, which Nintendo probably thought had an affect on Prime 2's initial sales. It was actually Nintendo's self-constructed misfortune of releasing Prime 2 in Halo 2's release period on a KIDDY konsole that lead to its sales tragedy.
MP3's linearity is just an extreme response to that. (dammit, I played the game with the hint system turned off, yet the stupid game still told me where to go!!!!)
Navigational hints should be OPTIONAL, as in the default would have no one tell you anything unless you accomplish something significant (boss, upgrade, something typical like that). A progress log would be sufficient.