I grew up a JRPG player, so alot of game design choices commonly seen in WRPG always irritate me
I don't think there is a satisfying answer to this question.
-Weapon/Armor degredation
Half way through a dungeon, my armor or weapon breaks. I didn't fail a puzzle, i didn't fail to exploit an enemy weakness or misunderstand the combat, i'm just being told to stop what i'm doing and go to a nearby town and have my equipment repaired while naturally playing the game. Why? There doesn't seem to be a lesson to be learned here, no mistake to be corrected, its just irritating me as a player and disrupting the flow of the game.
There can be several reasons for equipment degradation, some are fine, others not so much.
1. Sometimes It's just for realism
2. To limit powerful equipments use (like a medieval equivalent to ammo availability for that super powerful weapon).
3. If there is extensive usage of a crafting system, sometimes it's to encourage use of the crafting system. Relevancy of crafting systems in particular games are their own problem
4. It can also be to add challenges as the efficiency of equipment degrades, battles become harder - which is functionally similar to MP pools and the likes in JRPG's.
Sometimes though, it's exactly what you probably think it is. It's to pad out gameplay and bring content into large or open worlds whilst loosely satisfying the above 4 things, and it really isn't the best game design.
-Lots of loot, inventory limitations, and weight encumbrance.
This is another matter entirely. There are technical limits to how much inventory a game might want to be storing, so adding limits - be they a hard limit or weight encumbrance - is a perfectly natural thing to do. JRPG's also have inventory limits too.
Inventory limitations are not the problem here though. It's the loot, where a number of different problems can occur, such as:
1. Open Worlds in particular need content to fill into those worlds and this often leads to a lot of junk inventory while you're spending time exploring. I believe this has been discussed already in the thread.
2. Players not engaging with crafting or equipment customisation mechanics leading to a build up of junk in your inventory. If the game wants you to upgrade your equipment, and you're not really engaging with those systems because maybe they're confusing, or a poor use of your time when you can wait it out for something cool later, then obviously you're going to have a loot problem.
3. The game not balancing loot well, leading players to end up with a lot of junk even if they are engaging with crafting or equipment customisation mechanics. Often a result of mob drop rates being overly giving, or giving a lot of junk drops before giving you something good.
4. A disconnect between intended and player behaviour is another, for example; the devs intend for players to sort through chest loot for stuff they want. But players tend to just empty the whole lot.
It's not just WPRG's that have these problems though, Tales of Berseria for example is pretty well known for breaching the 2nd and 3rd problem. The equipment customisation system in that game is kind of confusing and unless you're on the highest difficulties it isn't really necessary to create custom gear that's powerful. Couple that with mobs dropping too many items on a roulette system (where you're mostly getting rubbish, but occasionally get something awesome) and you have a problem.
Atelier games have an issue with it too. Not because they're using bad mechanics but because players start to disengage with certain materials as they progress through the game, but because you don't want players to get the best materials from harvesting points every time, you end up with junk the game intends you to offload to merchants or reduce to gems. But after a point, players get diminishing returns, so the inventory builds up.
What causes it? Usually the developers know the games have these problems but just haven't been given the time to action feedback. Balancing is complex because it has to cover many different types of player, and predict how people will play a game. Also, how a game balances loot has to conform to progression. But, devs have deadlines.
