Since there seems to be a decent number of people watching this thread, I want to present a "prototype" idea for how to address at least some of the issues from the above lists.
The central concept is that we change the benefit of HQ ingredients, from adding quality to "reducing" quantity.
This goes back to my question on the Live Letter thread regarding whether we could substitute a larger amount of a more common item for a single rarer item, but extending that idea to crafting as a whole.
Let me provide an example to illustrate.
Suppose we are making an Iron Ingot. This recipes calls for 3 Iron Ore. If you use 3 NQ Ore, you start with 0 quality. If you using 3 HQ Ore, you start with 50% quality.
My suggestion is to make it such that instead of an HQ item adding quality, it simply requires you to use less of it for the synth.
Under this method, you can use 3 NQ Ore, and start with 0 quality. Or you can use 1 HQ Ore, and start with 0 quality. This assumes a general NQ:HQ value ratio of 3:1, so any HQ is worth 3x as much as its NQ counterpart.
However I did remove the quality bonus from the HQ Ore. Compensating for this is rather simple, all we do is cut the total quality for, well every item, by half.
Here is the end result.
Total quality required for all recipes is halved, making it "seem" like we are starting with all HQ materials every time, though really we just have less quality to crank through. This means that the end result is entirely dependent on the crafter's gear, melds, abilities, and "crafting skill". Everyone starts at 0, whether you are dirt poor and gathered things yourself, or are filthy rich and have an FC that just showers you with HQ everything.
For gatherers, this means that the NQ items you find ARE NOT WORTHLESS! They are just "worth less" than an HQ item... 3 times less... but that are still worth something!
And for adventurers (Tomes, Ixal Items, and Desynths), since these items are generally not available in an HQ form, then the number of items required will stay roughly the same.
Generally available items, such as Tome Mats and Desynth items will stay at the current levels. Time gated items, will require less, and perhaps come with an alternative item that could be used (in a higher quantity) to compensate.