I like the idea of increased complexity for nutrient balance. If ratios that work out to three (ie. 1:1:1 or 2:1), I'd be fine with a limit of 9 crops per tile, however, the neighbor requirement should be reduced from 4 to 3 to compensate, then.
Honestly, even typing this out, I think I see where Klei is coming from here. It seems their goal is to allow for completely passive farming, but the cost being not having any giant crops. If you want giant crops, you need to manually fertilize. In that regard, I think where this falls short is the psychological aspect for players where, if their self-sustained farms don't produce giant crops, the build is considered a failure (or at least inefficient). Maybe a compromise is to make giant crops a bit more obtainable passively, but less likely to have the biggest payout without demanding player attentiveness.
Edit: spent some time with the new nutrient balances.
So as far as I can tell, all the plants pair as 1:1:1. these are the two combos
onion/pepper : garlic/durian : dragonfruit/pomegranate
potato/eggplant/watermelon : toma/pumpkin/corn : carrot/asparagus
I'm actually a bit disappointed in the lack of diversity here. Every plant just consumes one thing and outputs the other two things in half the quantity. I liked it better when some plants consumed two things and output the third thing in double the quantity. I recommend bringing back the latter, but maybe reserve it for common trash veggies. This would essentially allow a player to choose either 2 crop types (with 1 being a trash type) or 3 crop types.