clunky inventory
Ok so yes I can agree that the inventory can get confusing with equiping stiff but other then that I was not bothered.
stupid side quests
As for dumb sidequest? Well there not the most fun I have seen for sure and they are mostly just killing things or gathering item's so yes it is not really innovative in anyway way but it is by no mean's dumb. This has been used in many game's and One thing nice about it is that if you accept quest you gain affinity with whoever is next to you which is very nice. (those of you who don't know affinity effect lot's of factor like being able to share each others attributes and such)
Also Sometime when you accept quest you may have already compleated them from previously finding items so suddenly your talking to someone then boom you just got a ton of money and experience.

But I do see your point tho. It can get annoying
Pointless gem crafting and overated battle system

This I could not dissagree with you more!? Have you actually played the whole game and crafted gem's? It is of extream importance. You can make your characters ten times stronger, higher hit points, Resistance to status ailments everything and without having to spend any money.
All you do is take your two characters that have good affinity and use the free materials you have collected and boom you get great gems. You can actually mix and match anything hp, power, ether, Whatever and mix them together for a great gem.
You can put them in your weapon or gloves, shoes, armor everywhere. Also depending on how connected your characters are you choose determines how strong the gems become and I have made some super bad ass gems. It's really not only innovative but and must for this game and literally will save your ass and make you extra badass!.
I can understand some of your other statements but on this one it does not really make any sense to me.