I have been trying to write a suggestion about "preserving" your inventory between levels. But, I can't figure it out!
Picking up a brand new item in a puzzle and always having it go to the first slot breaks the "muscle memory." I have no idea what would work better, though! 
Just remembering where items were previously breaks many more things, I don't know.... This is pretty minor though, I think.
I've thought about some sort of system like that, too -- basically, like how Zelda 3 handles it, with fixed locations for everything. Or actually most of the Zelda games (some handheld ones aside). One problem is that -- currently -- there are 41 unique items that you can find in the game. There's a handful more that we already have art for, but which aren't in the game. And if we do expansions for the game, we'll add more still.
Right now the inventory supports 25 items and that's it, so you can't have everything all at once (which is okay, because you never remotely do). The nice thing about this sort of inventory is that it's really compact. But as you say, it messes with muscle memory, which has been bugging me for a while, too. If I went to a fixed-position grid, the smallest I could do would be 7x7 instead of the current 5x5. That would give us 49 total slots, but that's only 8 slots for growth. If I went to 8x8 that's instead 64 slots. With that I could give some nice spacing to get the weapons, tools, and keys/maps/papers/etc separated out so that they don't get confusing too much.
The other thing I've been thinking is that with some of the non-usable items (things that you pick up and then you just have them), those could be moved into a separate section that is out of the main inventory. That would be the 9 papers, the golden book, the mirror, and the map. That would be 12 items we could reduce from the main inventory, which means that we'd only need 29 slots in the main inventory. If that was the case, then I could go with a 7x7 grid and 49 slots would give me as much expansion room as the 8x8 would have in the other model.
So, what do people think? Basically what this would mean is more moving around in the inventory to actually select things, but it would be something you could do from muscle memory. And the stuff you're likely to use most would be nice and compact at the top, anyhow. I think this is probably the way to go.
