"I love having to outthink a game, but when I'm walking through an area I walked through three times already, having to kill the same irritating enemy which I already killed three times, there's no thinking involved."
Did you forget the main character gets by, by shooting things? For like, the entire series?
"I love the puzzles and bosses (which ARE puzzles in their own right) in the Metroid games. They're clever and typically awesome, but the sheer amount of walking around between these puzzles and bosses was so boring that I couldn't finish it."
Puzzletastic bosses in Super Metroid? Hardly. Stop generalizing. jump, duck, and shoot. that's all.
You make walking sound like a bad thing. It's like you didn't try to traverse quickly or you didn't really know where you're supposed to go and you pay an excessive amount of attention to every square-foot of wall and floor you walk by. You talk as if you had to stop at every enemy you meet, have tea, spend at least 30 seconds strafing around it to hit the weak spot, then finally kill it. But all you had to do was jump over it and roll yourself to the next blue door (or screw attack, even).
But you are right that the inclusion of a teleport would alleviate the backtracking impression. But it would have to be lightning fast like Talking to Midna, and the locations not as generous. The teleport rooms in SotN and Circle of the Moon were handy, but I felt they took forever to reach, despite the 2D gameplay (Alucard was slow, and Circle had a more convoluted level design). All that other junk people mentioned about highlighting spots on maps would be helpful too.
Be careful what you wish for. I don't want MP3's game worlds to be a disappointingly predictable series of dungeon rooms with little to no branching, like what we got in Toilet Princess.
I personally like the convoluted nature of MP2. More places and more interesting ways of hiding secrets, and less gigantic arena rooms with big pockets of empty air space.
EDIT: Is that the best crab you could find?