Ian, I think the difficulty issue with modern games is that due to their cinematic and scripted nature replays are frustrating. Getting on a roof and seeing your character perform a cool stunt to get to the next area is cool once, meh the next few times and just a waste of time after that. When you lose you don't hit start and have fun again, you trudge through areas that were only interesting the first time and the story is repeated for those parts. Plus 3d games are often slower than 2d games because it takes longer to orient yourself, in 2d a firefight tended to be over in one hit, in 3d absolutely everything has a long health bar. When replaying a level in Ninja Cop and knowing where the enemies are it was mostly a matter of one-hitting them because enemies died in one hit (though getting that hit in could be difficult at times), in a 3d game any fight is going to last much longer because it's all about combos and stuff that need to be applied. Additionally combos feel less awesome than one-hit-kills (in part because combos tend to be just button mashing that gets illustrated by the game to look like a variety of moves).
As for E3, Nintendo's goal was to eliminate any advances from MS and Sony onto their turf (hence the motion plus announcement before the first keynote) but there were no attempts so Nintendo's defense was useless and people complained that they weren't stepping on MS and Sony's turf instead. Had either competitor made a serious attempt at grabbing the new market while Nintendo was busy appealing to core gamers instead it could have meant defeat for the Wii.
Difficulty of programming isn't much of a cost factor, programming is fairly cheap (unless you're trying to optimize complicated algorithms but even then it's usually fairly cheap compared to the graphics budget and this doesn't seem like it'd need much optimization).
As for secrets, I think it just hints towards the closest "problem" when you hit the button, if you're just in a passage (or just generally far away from anything unsolved) it probably wouldn't do anything because there's nothing to do there. When you're in front of a secret puzzle it'd probably help you with that too since it's the closest thing to your character. Not sure about secret bosses though, those tend to be extra difficult precisely because they're secret and I think a hint function would be misplaced there since it's an optional extra challenge (the hint should be "go away until you're good enough"). Generally I don't think it'll solve things on the other end of the world, just the things in front of you. If you don't even know the general area you should be in they've usually provided you with a potentially obnoxious helper (Hey, listen!) that will give you some general directions.