Asking for a specialization system wouldn't solve whatever problem it's supposed to fix, it would merely postpone it for a few months to a year because it doesn't force a player to specialize, it just forces one of their characters to specialize. Alts are a thing. In other MMOs where you can't do every craft/class on one character it is fairly common to have multiple alts to cover many/all of the other options. One of my favorite things about FFXIV, even back when 1.0 launched, was that I didn't need an army of alts anymore. It's one of the biggest reasons why I even bothered to check out ARR when I heard it was getting relaunched.
If you want crafters to work together, make crafts that require more than one crafter to perform the synthesis. Things could really get interesting with a system involving something like that.
One of my current complaints is that HQing the highest level crafts is currently too easy (can use all NQ mats while still being a fair bit off of capping stats, nevermind how easy it is with capped stats and HQ mats). I'm not sure if the crafts were 'balanced' around people only having one 50 craft (like 1-50 + Ifrit was apparently balanced around people not having all their cross class abilities), and crafting 55 HQs should be possible without a bunch of cross class 50 abilities (15 cross class should be assumed). One way or another though, gear is so laughably easy to HQ that tons of people can do it for even the 'hardest crafts' without major investments in their crafting gear/abilities, which results in the market being easily flooded. It could make a little bit of sense with higher item level crafts being planned if we aren't getting new crafting gear any time soon, but that list of items will be pretty small (in comparison to all the items available to be crafted) and the market for them will be even smaller.
Basically, HQ mats need to matter (current ease of HQing with NQ mats really isn't doing any favors for gatherers, either) but HQ mats currently don't matter for any crafter that's set up remotely decently.
I'm a bit concerned about furniture, too. I doubt it'll really help crafting all that much other than for a week or two during the initial rush. If it's like dyes/fishing lures and there's no reason to HQ it/can't HQ it at all then any idiot that bought their way to 50 with leves will be able to make the items with no issues. Much like people practically give away melding since the only requirement is being high enough level. Even if there is a HQ benefit (aside from the issue of HQing being a bit too easy), I imagine furniture recipes will be spread throughout the levels so everything sub-50 will be easily made anyway. It is nice that it'll be something that crafters, gatherers, and combat focused players will all want - just a little worried about how easily the market might get flooded and crashed.
As for the gear vs dungeon drops, several good points were made by other people as well as some by Yoshi. The concern of people being able to buy gear equivalent to what a dungeon drops before entering that dungeon is very valid. The tome (not gil) cost of crafted vs darklight gear is also out of whack, not even considering the extra cost/effort of melding.
The idea of BoP materials combined with a "request craft" option similar to the melding request feature was a good one (with the item itself being BoP, so that only people that have done the dungeon would be able to use the gear). If the mat was tradeable then regardless of the crafted item being BoP or not, people would be able to get the gear before entering the dungeon. If it required the person to have the craft themself, it would force people that may not want to engage in crafting to level a craft (aka, something they view as not fun) to get the gear they actually want, devaluing the effort of dedicated crafters. Not to mention it would force people that may want to just engage in crafting to run high level PvE content to get those BoP materials.
That said, the suggestion someone had about crafted items being Best in Slot for some slots, but not all was a great one. Especially if combined with the above so that people couldn't get gear equivalent (or better) than raid drops before even doing said raid.
Lastly, RMT. You can't really design gameplay to stop it. Runescape tried to do so for years and it failed miserably (many of the attempts only served to annoy honest players). Eventually they got smart and put some serious effort into anti-bot code that seemed to work fairly decently (ongoing battle of course), with the added bonus of not irritating their actual player base. Any time someone doesn't have instant gratification and they're willing to pay someone to provide it, things like RMT and run sellers will exist - and designing a game to be nothing but instant gratification would close off a lot of interesting options and depth.
In any case, I've found the crafting system pretty enjoyable (having not been a heavy crafter in other games) which is why I kept engaging in it, especially with gathering many of the mats myself as it gives me reason to travel all over the world rather that just sit in town or in small handful of dungeons. Done the MMO combat thing more than enough in the past. I just find the crafting 'endgame' to not be as fully polished and fleshed out as the leveling experience felt.