In my opinion, almost everything aside from story and dialogues in The Witcher 3 is average or below average. But if I had to pick one thing to change, it would be loot, items and their levels.
There are countless of ? marks on the map, but there is almost no reason to go to them. They are nameless locations without any touch of lore and loot there is worthless most of the time. If you go there early, you get junk items that can be only sold at merchants. When you go there in the mid or end-game, you can get crafting items, that you most likely already have tons of. Sometimes, there are special items, but they are locked behind levels and there are quests that will take you straight to those items, so once again, there is no reason to get them early, since you can't use them.
Speaking of levels on the items, why are there levels on the items? That's just so stupid mechanic. Do you want to tell me that two identical swords are not identical? If there are stronger versions of the same sword, why doesn't everyone have this stronger version? How can anyone even tell the difference?
I would change it to similar systems like in Gothic or Kingdom Come: Deliverance, where exploring actually mattered and could drastically change the difficulty of the game. You could get the best weapon in both games super early and you could even use it, if you have good enough stats, but both games were still challenging and fun to finish.