I appreciate you saying things are slightly stale - I agree with that. The game isn't dying or doomed and hasn't made suddenly bad decisions of late, it's just doing the same thing that has worked for a decade. And it's working even now...but it would be nice to get some change to make it a bit less stale.
1. I'm not sure what started that, honestly. I think it was the tomestone grind. They went from being something you did for quest progress or gear drops to something you'd run over and over again, so people wanted that streamlined because gamers are often all about efficiency and the lowest chance of failure. I honestly loved the old Hard dungeon system where the story would evolve a little, and wish we had more of that. It was also nice getting 2-3 dungeons per patch instead of just the 1.
2. I honestly don't know the best answer here. Different games have done it different ways, but WoW has had token gear since at least Wrath, and I think maybe BC (where the Season 2 PvP set was actually decent spot fill slots for entry raiding). Before that, there were "Dungeon sets" or "tier 0.5/1.5, etc", though they basically ended that system during or after BC. I do agree it'd be neat to have dungeons you might want to go to to get a piece instead of just grinding tomes or taking a trip to the MB. It's also kind of a shame that dungeons have this gear, but no one uses it other than for glam or that alt Job "I'm planning to play eventually but not right now". Granted, gear in FFXIV also doesn't have set bonuses or anything (other than the level 50 GC gear.....). I do think tome gear is good as spot fills for RNG, but it'd be nice if that was more the "backup" option than the "main" option.
3. I'm mixed on this one. I think it's fine, but I'm also drowning in glamour prisms and have around 800 items (or more) between my chest and my inventory/armory chest/retainers. But I also somehow really hate the WoW/GW2 interface where it shows all the gear and wherever you get it and seems to be an immersion breaking checklist system to me somehow. I really don't know the answer to it, honestly. I still remember getting that cool red one shoulder guard chest and shoulder piece from the desert in WoW around level 40 or so that looked like Dart from Legend of Dragoon.
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Other things:
A. Need midcore/mid difficulty content. We really don't have it. Extremes have edged up to Savage difficulty and everything else to MSQ/normal. It'd be nice to have a "Hard" mode difficulty in between those and for Extremes to tone down the body checks.
B. Exploration Zones! Bozja/Eureka were divisive, but they gave people things to work on when they were bored and had downtime.
C. Rework encounter design and Jobs to where healers do more GCD healing and "heal checks" aren't just "mitigation checks".
D. Dump the 2 min meta and embrace more diverse Job designs again so everyone can have at least something they kinda like, ideally at least one Job in each role, but at the very least, a Job that they really love, but without leaving anyone out in the cold with nothing. Don't take away what people have and love in the effort to change things. Is this hard to balance? Sure, but as long as it's relatively balanced, then it's good. We need to embrace heterogeneity and just accept that min-maxers are gonna min-max no matter what, so let them and let everyone else have fun with non-homogenized Jobs.
I think I'd start with that.