That's exactly what I mean.
It's why I hated PoP so much too.
"This is how you do the puzzle. Now go do it, then fight a little, then we'll resume our half-assed attempt at an epic story and then tell you how to do the next one. Don't worry, you can't die, all you have to do is press L. Unless you're in a fight of course, in which case... how lucky are you feeling today?"
And MP was perfect... the story wasn't intrusive. There was almost no story if you didn't go out of your way to read up on it, and if you did the story and background details were actually pretty good stuff. You rarely ever lost control of Samus. The only problem I ever had with that game was the last escape sequence.
But that's not all I meant. What I especially hate is when stupid developers try to pull off a deep story. It never works... MGS2, the FF series (especially FFX), Xenosaga are cases in point. Those storylines insulted my intelligence, not because they weren't deep, but because they tried to be deep and failed miserably. I'd rather have a story that makes no sense on purpose.