Oh-ho, you make some delicious points~
Many games fail to include decay at all. Although it would be fairly easy to add. Cataclysm shows the style the best - every X multiple of turns, you make a check on certain things that aren't time sensitive. Like, every half hour you could check the decay rates on items and reduce it by 1. When it hits zero, rot it, or collapse it or break it or whatever. This could of course be tweaked for any number of things. If it's outside, give it a decay of 2 per tick. If it's inside, give it 1 per tick. If it's in a basement, give it 50% chance for 1 tick. If it's in a basement in a barrel and it's salted, give it 10% chance for 1 tick.
Tools could incur a very slow natural decay, but also add to their decay on use, which could get interesting. Iron tools may have a high durability, but if left outside they incur rapid decay due to rust. Meanwhile copper could be relatively soft and weak, but incurs a very slow decay rate outdoors, because copper doesn't rust. If I were going to handle tool decay (and I will) then AI would probably make an influence too. Agility/Dexterity may allow a user to avoid a decay roll, so that skilled people are less likely to mangle their tools. So you'd probably end up with that one employee, strong as an ox, loyal to the core, but... you don't quite want to give him the shiny new steel shovel.
Disease of crops and animals will definitely be in. Burning cow corpses is a high probability, that's the only way to make sure it won't spread. *Shrug* or leave the cow corpse out. Maybe the neighborhood night terror will eat it and become sick and not visit you as often! Not as many fun options with crops though. Just gotta burn the field I guess!
In other news though, I've managed to make the map follow the player now! It was unusually tricky to find the math for this, but it looks much better.