Welcome to the game! It's always nice to get new blood in the community.

I hope your enjoyment of the game is enough to offset your annoyances. The game can obviously be benefited by some QoL improvements but is still a great game and has come a long way since 1.0 and even 2.0.
1. This one I honestly don't notice too much. When it comes to crafting, it's mostly about prep-work; I either just make sure I've already got what I need on me or I hunker down somewhere near a retainer bell/MB and work there. I don't know if I'm just used to the system or what, but I've never really had a problem with the inventory aside from item bloat. (Seriously, for an omni-crafter the two default retainers are just not nearly enough space.) My husband, on the other hand, played a lot of Guild Wars before coming to FF14 and complained long and loud about not being able to craft with mats that weren't in his personal inventory, so ymmv I guess.
2. ... Is your monitor set darker normally? Or it could be a video card thing, maybe?
...
5. Not sure why this would be a thing. As someone who played a lot of MMOs in the past where you had to walk
everywhere, the aether shards in the city already seem like a huge luxury to me so walking 20 feet to the nearest one doesn't phase me. It would admittedly be nice to mount up in the cities but with the number of people who think it's funny to block NPCs with huge mounts, well... "this is why we can't have nice things." And the aftcastle aethershard's placement has always seemed a little off to me too. But heck, we finally got one in Ul'dah next to the MBs, so maybe there is hope for SE changing that one around too!
6. I'm not even sure what you mean on this one, sorry.

I just click yes with my mouse, or are you on a console? I've no idea what the UI is like there so I can't comment on this one.