Loftar has recently mentioned that he'd like to redo the crops, so I reckon this is a good time to discuss how it could be done.
First, I think the whole method of raising crop q should be scrapped. As I understand it, seed sorting is supposed to be a minigame, but if it's got just one solution (and an obvious one, to boot), it's not really a game. So, all seeds should be the same quality if the crops are grown in the same conditions.
Next, scrap the item representation of seeds and replace it with "liquid" representation (works like liquids do, but uses kg as unit of measure). Give seed bags a fairly large capacity (100kg or something), and have them average out the quality of their contents (but really average, none of that what happens with troughs). Allow grinding of whole bags of wheat at a time if one is using a millstone as opposed to a quern (windmill or watermill required). Have flour work the same way, so that instead of using 1 flour (seriously, what is 1 flour?) different recipes call for different amounts of flour (.5kg for a loaf of bread, .2kg for a cake etc.). In addition to sacks, a new silo building should be able to store stupidly large amount of seeds.
Now, on to raising q. Quality of crops should be the average of the seeds and the soil quality, dragged down by farming skill if it's lower than the result. Soil quality should be improvable with manure, compost etc. It should be possible to push crop q beyond the soil's q through a minigame of sorts (how else do you get compost better than your soil?). Basically, your crops demand certain things (water, weeding, soil ph adjustment with limestone etc.), and each time you fill one of these demands they get a point or three of quality beyond what they would normally be. The number of these demands you can fulfil in one crop generation is limited by your farming skill (has to be higher than crop q to get any at all). Much like numen you can forfeit a demand, but that would still expend one of your q raising chances, and maybe even knock out some of the progress you've already made. Like numen, you should get a new demand (if you're eligible for it) as soon as you fulfil the previous one, so that you're not forced to log in at specific times to tend to your crops.
Due to the above thing, growing time needs to be longer. I think something like 2-3 RL days would work fine for wheat, so you can squeeze in two crops per year if we get seasons (I reckon a game year will last something like 10RL days). The crops' yield should be increased so you get roughly the same return for invested work, only now there'd be work other than ploughing, planting and harvesting. The general idea is to increase diversity of tasks involved in raising crops, which I think would make farming more fun.