I'm with Andail on this one, although that has much to do with the fact that I somewhat dislike the fact that most adventurers seem to suffer from acute case of kleptomania. I mean, sure, it's a genre convention and all, and it's completely fine(even charming) for LucasArts and Sierra style comedies, but if your game is supposed to be more realistic and serious in tone - that's where it starts to get quite problematic. It's not only the question of player's comfort and how does the puzzle work better, it's also about the immersion and boundaries of an in-game logic. After all, is it the player who tries to pick everything up, or is it the main character? And if it's the latter - what's wrong with this person? 
To be fair, this is true for the whole "inventory puzzles" system, not only for the "picking-up everything that's not nailed-down, and if it is - use the crowbar to unnail it first and then pick it up" aspect of it. Blackwell games(and Gemini Rue with Resonance to a slightly lesser extent) are very good at avoiding those, while still remaining point-n-click adventures at heart, so I guess it's a problem that can be avoided altogether with a good design, but it's still very much a matter of context.
It also depends on the interface, of course - if you have a "Pick up" verb it would be quite strange not to let the player pick it up, but if it's a two-click interface - it gets a bit weird.
The main decisive factor here should be, in my opinion, the weirdness-of-the-action-to-be-performed to weirdness-of-the-game ratio. For example - picking up a random rock can only be considered slightly peculiar(4/10 weirdness) and wouldn't raise eyebrows even in a moderately serious game(3/10 weirdness). 1.33(3) is a pretty decent WOTATBP-to-WOTG rating in my book. On the other hand, tearing apart a whale carcass with your bare hands for no apparent reason, but finding a golden ring inside is a tad more disturbing(9/10 weirdness), and might be considered strange without the prior knowledge of the golden ring's location (if you know it's there, though, it's a completely sensible thing to do
), and wouldn't fly even in a slightly sillier game (5/10). My rating system could use some work, yes.
To be fair, this is true for the whole "inventory puzzles" system, not only for the "picking-up everything that's not nailed-down, and if it is - use the crowbar to unnail it first and then pick it up" aspect of it. Blackwell games(and Gemini Rue with Resonance to a slightly lesser extent) are very good at avoiding those, while still remaining point-n-click adventures at heart, so I guess it's a problem that can be avoided altogether with a good design, but it's still very much a matter of context.
It also depends on the interface, of course - if you have a "Pick up" verb it would be quite strange not to let the player pick it up, but if it's a two-click interface - it gets a bit weird.
The main decisive factor here should be, in my opinion, the weirdness-of-the-action-to-be-performed to weirdness-of-the-game ratio. For example - picking up a random rock can only be considered slightly peculiar(4/10 weirdness) and wouldn't raise eyebrows even in a moderately serious game(3/10 weirdness). 1.33(3) is a pretty decent WOTATBP-to-WOTG rating in my book. On the other hand, tearing apart a whale carcass with your bare hands for no apparent reason, but finding a golden ring inside is a tad more disturbing(9/10 weirdness), and might be considered strange without the prior knowledge of the golden ring's location (if you know it's there, though, it's a completely sensible thing to do
), and wouldn't fly even in a slightly sillier game (5/10). My rating system could use some work, yes. 
). It's just the way it's made - there are no "wrong" interactions in this game, so when you're trying to use an object on something you're not supposed to be using it on - nothing happens (and if it's the right interaction the object-cursor would become highlighted, so you can always tell what you can and can't do). So, you are only able to combine the items that are meant to be combined and share them between the characters only if they are meant to be shared (and I think there is only 1 sharable object in the game, and even that one is optional). Sorry if it's a bit confusing, it was done this way to cut down on the "Can't do that" responses and to streamline the gameplay. 
