Basically it goes like this:
In 3.5 if your players were using the crafting skills as written, then they were doing it either
a) Purely for roleplaying reasons: there really wasn't any benefit to crafting something yourself. The money you saved was simply not worth the time.
b) Because the wizard had mandatory downtime, and you had nothing else to do with your time.
c) Because you wanted to get something that the DM wouldn't let you get out of the shops
d) Because you were cheesing out fabricate
...
That said, if you can come up with a feat that is purely beneficial to the character that ALSO helps with flavour, that's a totally different kettle of fish.
Finally - you mentioned that you allowed craft checks to produce magical items from magical components - well, that's pretty much what the enchant item ritual does. If you're willing to tinker with it a bit (ie - if you require that the PCs get specific items to perform enchantments), then there's no reason that you can't remove it's level restriction and use it to fuel quests (as I presume you're doing when you send the PCs to get components). I think the default level restriction on it is there simply to make players appreciate the magic items they find more in the first few levels of play.
Agree with your whole post, but want to extend it. The two really good reasons to have craft skills in a game:
1. The game is very focused on the mundane, and thus crafting is vitally important. You are far from town, there isn't much if any magic, and you need some more arrows to restocks your quiver. Scrounging for materials to mix with your recovered, damaged arrows becomes interesting.
2. At the opposite extreme, crafting is important because there really isn't much in the way of mundane. Magical arrows are practically required for anyone fighting something tougher than goblins or ogres. So if you are dedicated archer, you better be able to roll your own. "Enchant Weapon", let alone "Enchant Magic Item," is thus perhaps too broad for what the game is about. There really aren't any mundane crafts, because in this fantastical world, everyone uses a bit of magic. The maid needs a magic duster, maintained by herself, to possibly handle the level of dust thrown around by events. And ideally, all these magical crafts that replace the mundane are a bit dangerous. (That is how the maid became a 5th level commoner, BTW.)
D&D has never really been solely either of these things, though I'm sure some people have almost played it as the first, at low levels. And early versions definitely went after a bit of that vibe in their "operational" play, with sacks of provisions, 10' poles, and the like. Still, even then success was often based on operational concerns, but realized finally on having that magic wand with 3 charges left or that one extra healing potion -- i.e. the fantastical. Likewise, even 4E, one of the more fantastical versions, hasn't seen fit to require dangerous, magical feather dusters.
Basically, to discuss the role of mundane crafts and professions in a fantastical world is to imply some balance of magic as technology, or magic as a counterpoint to technology. If you want to do that, then the implications are far more pervasive than whether or not you have craft skills and what they do. There is nothing wrong with adding craft mechanics to 4E, of course, but there is something rather myopic about getting so caught up in that issue without seeing the larger implications for it mattering.
