The seed sorting component of crop breeding is pretty frustrating for me. Because the cropnalyzer only works on seeds in your hotbar, there's a lot of fiddle just swapping seeds out between the hotbar and the inventory to get them all scanned. As you say, the lack of stats in the tooltip and the identical sprite for all seedbags means that if you don't keep careful track of your scanned seeds you'll get into all sorts of mess.
I presume it's a hurdle by design to pad out large scale crossbreeding. It's important that high-scoring hybrids are quite hard to breed or there'd be no satisfaction in agriculture. I respect the decision of the designers and the fact that nobody wants a 'win' button on their game, but I hope that Al or one of the team has tried using the system for a few hours themselves.