With regards to your puzzle bypasses, taking the idea of the magnet as an example, you said you can make a magnet which is an inventory puzzle or you can find a magnet which is a research puzzle, which encompass two different types of adventure games, your Monkey Island style game, and your Sherlock Holmes style game, which is no bad thing as it could then appeal to both sets of fans, however it'd be a lot of work because I suppose you need to somehow close off one avenue of investigation when the other is taken to stop confusion over having two magnets, and you have to make each route complicated enough to appeal to those fans, for instance if you found a log on a person it probably couldn't simply have the locker code, it'd have to have some sort of 'treasure hunt' that leads you to the locker code via a couple of other clues. It's a very ambitious project but you don't have a publisher ramming a deadline down your neck so i say go for it!
And with regards to your object use, I don't know if this sounds like a good use of inventory, but I sometimes think about making a zombie survival adventure game where you'd be in a room and there'd be objects you could pick up, but each object would have real world uses, taking a cue from Resident Evil Outbreak. So if you picked up an axe you could use it to break down the door to the next room, or you could smash up a table to then use to barricade the window, or you could use it to kill a zombie who'd gotten into the room, but at some point it'd break so you'd then have to find some other way to do one of those three puzzles. I figured it'd be a nightmare to code but i think that would be an ideal adventure game in many ways as you'd rarely ever get the "i can't do that" for something that in the real world you could actually do which is the holy grail of adventure gaming.
anyway i've gone off on one a bit now
