Vesper, I love all of your ideas, and could propose even more and further ones in the same line.

However, I fundamentally disagree with implementing these ideas via the restrictions that you suggest. Specifically, you state:
Each character can choose ONE master craft, TWO advanced crafts and can rank every other craft, but it would be considered a general craft.
Why is this a preferred method for limiting what a crafting character can achieve? This is (as was pointed out above) entirely contrary to Yoshi-P's stated desire of "letting players play as they like". Further it doesn't prevent a player from creating multiple characters in order to master multiple crafts. Instead, it caters to those with the wherewithal to pay for additional accounts / characters.

I would propose taking all of your suggestions, and making them individually unlockable abilities via "quests". This replaces the somewhat arbitrary limitation of "you can only master one craft" with "you can only master what you are willing to invest time in".

Example:
One of your recommended attributes relates to HQing of materials/items. You propose General to access only +1, Advanced to +1-2, and Master to +1-3. I feel that this paints too wide a stroke. Simply by achieving 'Master' within a particular craft, you now have access to make +3 items of EVERY item within that craft. Why not restrict to +1 in general, for any item above rank 50. Then create quests that allow Advanced status to a particular class of items / materials -- thus allowing for creation of +2 items, but only for that class of items. Further, it could only unlock for items in the rank 51 to 65 range. Then, allow an additional quest to unlock Master status, allowing for +3, again for the particular class in the particular range.

For items above rank 65, further specialization of item types could occur, again requiring specific quests to unlock access to create +2 and +3 items. This branching factor limits a single player from mastering every single aspect of every single craft, while maintaining the freedom (or illusion of freedom, if you prefer) to choose how to advance your character.
A single character could master different specialized aspects of a myriad of crafts, or could choose to concentrate within a single craft, as the player wishes. Looking over your list, I don't see any feature mentioned that couldn't be purchased via this "a la carte" system rather then lumping them together into "packages" and then placing restrictions on the number of mastered/advanced "packages".
  • Advanced and Master Recipes - quest to earn the ability to use these recipes within a recipe set
  • Facilities access - quest to unlock access to these facilities for use with higher rank recipes
  • Recipe variation - quest to unlock access to recipe variations within a given recipe set
  • Dying option - quest to unlock access to re-dying items of a given classification
  • etc

As the game evolves, I could foresee this progressing to the point where, at the advanced ranks (around 95 to 99), there could be quests involved to unlock the ability to use a single recipe. At that degree of specialization, the investment would (hopefully) be worth the achievement. If it were to take two days worth of time to unlock such an advanced recipe, and then a further two days each to unlock +2 HQ and +3 HQ for that recipe, that is an investment of 6 days. If there were 20 such recipes per class, representing 160 recipes in total, that adds up to 960 days to master all such recipes - well over 2.5 years. This would be in addition to recipe styles and variations, not to mention playing DoW/M classes or ranking up the DoH class in the first place. However, it retains a sense of individual achievement for each player. An investment of 6 days to be able to create a particular high-rank item is very achievable.

In summary, while I agree with the your ideas, and the need for encouragement of specialization for economic reasons, I don't believe that restricting to a single Mastery is the best way forward.