All right, a new version is out. I've removed the combat skill increases, but left the leadership skill increases in.
The next big question: which reactions need to be given the option to choose specific reagents? Brewing? Milling/pressing/plant processing? Dying? Leatherworking? Stonecrafting? Carpentry?
My personal opinion is that only the reactions where it makes a real difference, where there's no other way to specify what to use, and where there are only a few choices, should be considered for the honour. Brewing doesn't need it, because you can already specify what plants your dwarves are allowed to brew or not. Stonecrafting ditto, and there are also way too many different stones for it to be practical. Leatherworking doesn't really care what kind of leather you use, since they're all pretty much the same.
The only reactions where it makes much sense, I believe, are milling and dying, and those only barely. If you want your military to all be outfitted in red cloaks, say, there's only one way to do that right now: buy the materials one by one from the caravan, mill everything in your fortress until you get enough red dye, dye cloth with all your dye until you get enough red cloth, and then make cloaks with all your cloth until you get enough red cloaks.
Of course, it's not possible to specify custom reactions at the dyer's, so I guess it'd just be milling.
Your thoughts on the matter?