(mild spoilers) All in all, I agree. The biggest issue for me, is that I have loads of runes for two sets of weapons and armor. It isn't so much that I get loads of swords and armor pieces from fallen enemies, it's that they have near identical stats. It's just vendor fodder and it doesn't make the game any more interesting.
For instance, examine Borderlands. As an example, the enemies tend to drop a small variance of items. One enemy type will always drop very similar items, in the case of Witcher 3 one specific enemy will drop Nilfgaardian swords while another will drop a Skelligian Aketon. This happens in Borderlands and other loot based games. In Borderlands however, even though one gun might be very similar in appearance to another gun, while it's not "rare", the gun might be 10x superior, statistically speaking. This is where it's lost in the Witcher 3, in my opinion. Too many items are very samey. There are very evidently superior weapons that you can get through crafting, that just makes anything you'll find on an enemy not worth picking up.
That's the big thing for me. Once I get those weapons and armor crafted there is no motive to pick up weapons or items, because we don't need Crowns for very much else. At a certain point, after making some of the Witcher Gear, I basically just banked well over 30k Crowns and I have no reason to spend any of it. I kept picking up weapons and armor and ingredients, and didn't realize I don't really have a need to sell anything because I don't have a need to buy anything.
The only thing I can see myself truly needing Crowns for are respec potions, Alcohol for meditation potion regeneration, and Gwent Cards if I find any merchants that have cards. Am I missing something? I have well over 100 Dwarven spirits, not to mention all of the others spirits that are more rare, but not really rare. I go to an unexplored location and there are a bunch of lootable barrels, and each one has at least one Dwarven Spirit in it, amongst other things..
I tried to sell off all the small time alchemy/crafting ingredients I didn't need, but it's hard to say what I didn't need when I didn't know what I didn't need. I know I would need to save some monster hair to craft a specific item once I hit a specific level, but I didn't have any indication if there would be other diagrams that I would pick up that would be better than what I crafted, so I hang on to a significant amount of alchemy and crafting ingredients. I sell off a lot, but I try to keep 15 of everything, just because I don't know what I would need.
Making those ingredients meaningful? An easy solution. Give very small percentage (0.01%) exp bonus for each group of enemies slain, and (0.01%) for bigger monsters (fiends, elements, etc..). Meditating resets all your potions, toxicity and what not, but would also reset the exp bonus. Now, say you have the Enhanced Swallow, and you don't have any more charges left. Instead of meditating to refill your Swallow, losing your exp bonus, that you have alcohols and other alchemy ingredients that can be used to refill your swallow, and only your swallow. You get far less out of the alcohol, because it's refilling one potion instead of all of them, but you're also keeping your exp bonus going.
That would give you a reason to continue looting and picking up ingredients, and it stops you from selling off too much ingredients. There is more incentive to it than just "well I guess I could always use more Crowns". I believe Witcher 2 had a similar alchemy system in that you could craft more potions on the fly, but it's been a while since I played it, so I can't rightly remember the exact system.
As for weapon and armor. Perhaps they need to drop less, because everything is relatively samey. It's hard to say. If those items dropped far less frequently I could see people with progression problems due to finding nothing worth while to use in combat, and lack of funds to buy better gear because they can't find any gear to sell off. I feel as though the big issue for me playing through the game the first time was that durability didn't matter for a long time. If I had a damaged sword I could just replace it with one of the other six I have from that location that were just as good.
The over abundance of weapons and armor made the durability seem like an unnecessary element to the game until you get much, much deeper in, when you have the best gear for your level. At that point you just need to keep them repaired. Up until that point it was usually not an issue in no small part because I could go to areas where even my highly damaged sword would just chop anything down because I was severely over leveled for that area. It wouldn't matter how broke my sword was.
To that point, I feel like the biggest issue with the game was that nothing scaled with character progression. Please make it harder? It's a shame that I just became an unkillable god. Even looting in cities, right under the noses of the city guards didn't prove to be a challenge. Despite the game telling me these enemies were very dangerous. I just go into a Whirl and everything would die, playing on second hardest difficulty. How am I to believe that Geralt was killed by a child wielding a pitch fork when he spins in a circle and guards that are supposed to be very dangerous drop like flies? I'm an unkillable god in this game.
