I had this idea, which should work in concept. Feel free to use it. I'm posting a link here, as I didn't want to make a duplicate post. The idea and execution are posted on the Mods board. If nothing else, it might give some of you guys an idea to incorporate into your own mods.

http://www.gamesas.com/topic/1355733-wipidea-dig-your-own-mine-immersion-mod/

This looks like a really cool idea. Maybe after I finish the mod I'm working on I'll get started on that.
What I'd like more (and maybe this exists) is that crafting trees would give experience towards your next rank in some way proportional to the value of the item you create.

I know what you are talking about, and I had something in mind about that as well. To me, smithing/enchanting/alchemy shouldn't be skill trees, or at least should count toward your level. They should be placed in their own category, and to that category you should add cooking and hunting as secondary skills. Each of those "skills" would then have a variable assigned to it, and activities in those skills would increase that variable (like experience). Cooking a simple food would add +1 to that cooking variable, and once you hit 25 in cooking, you'd get a slight food duration buff to all foods you made from that point forward. Obviously, harder to create foods would be worth more points, and the decent enhancements to cooking (new recipes/better buffs) would not be given until a pretty high number (500-1500). This would be a good "poor-man's skill set", since you wouldn't have to create a new skill tree. Also, the skills increased this way would be outside of the leveling system in game.

Technically, I believe you could use this same variable system to replace the current smithing tree/smithing experience, and just have the smithing perks granted automatically at certain pseudo-smithing increments (50 points unlocks the steel perk, 150 unlocks elven and dwarven, etc). You could also do a smithskill check on item creation to see whether the item created is of suitable difficulty to grant experience.

Hunting could probably be added by adding an OnDeath script to beasts. Perks of hunting skill increases would be additional materials harvested from the animals, the ability to place bait (add a behavior to all carnivorous animals that attracts them to "meat bait"). The same behavior type that has npcs pick up what you drop would have beasts go pick up the bait you dropped (within a moderately long range) and "eat" it. You could use a grain bait for the herbivores. High level hunting would allow you to collect trophy heads, which could go to your house, or be sold.