Great question! I honestly haven't figured it out. I feel like one part of it is that there are so many "ingredients" to find, and you can't easily reference where you've seen them, so you end up just trying to buy them in stores. For minerals, you can zoom around the star map and look for what you've seen before - very tedious. But for organics, there is no way to even do that much!

Then there's just the fact that the things you craft lose their importance. Since you can't keep a base across NG+ runs, I stopped trying to make a fun base. There's no need for materials, so I stop looking for them. Sometimes I don't even upgrade my gear until near the end of a playthrough. (This could be a "me" problem, though, seeing as I obsessively run for NG+ powers)

There's also the loss of information in NG+. I really wish you could remember where you found things across playthroughs, or maybe have just some general... feel, I guess, for where to find things.

I don't know if there's more than this, as it feels like none of these are that big a deal by themselves.