I'd get rid of the mechanic of getting unnecessary doubles. Specifically with randomized drops/rewards. I play Animal Crossing as a part of my daily ritual sometimes. I'd check for new recipes, get duplicates, and stop playing for the day. It's just not fun to reduce a game to work like that.
I don't think that there shouldn't be any chance or grind involved, but I think an invisible coding quirk that makes a new or desired item inevitably drop would go to reduce some stress.
I think sometimes grinds like that can really mess up people who can just dive into games or have that compulsive desire to get 100% completion.
At least when I'm designing systems that nobody plays, my argument for using D6 pools is that even your grandma has d6s. Also less flat than a single other dice (d20). Also rolling d4s feels crap. Also, a lot of the mental arithmetic of adding a bunch of minor bonuses can be handled by putting dice in your hand instead of remembering the numbers.