On the note of crafting, keep in mind that artificers
do get a homunculus that's explicitly meant for crafting while the artificer is adventuring
Regarding the throwaway sword issue, what I've done in one game is change how weapons work drastically. Weapons aren't +1, flaming, etc, etc. Instead, PCs get a sort of "adventurer's spirit" or "hero's soul" or whatever they want to call it that get's upgraded and improved as they adventure. They spend the gold and train, meditate, pray, whatever, and gain the enchantment not on one weapon but on whatever it is they're wielding. Keep in mind this period of training/meditation/etc has it's time cut short from the typical time needed to craft, but still takes awhile - we've more or less abstracted it to "you can't train in the middle of an adventure unless there's downtime."
Weapons in turn come in three variaties. Common weapons can't take the self-enchantment - they're the standard, +0 nonmagical weapons, and can't progress past that. Masterwork weapons can take the enchantment. And magical weapons are all artifacts or legendary or - well, you get the idea.
In practice, it means that a fighter PC might have +3 flaming as a self enchantment. That means if he has a masterwork spear, it counts as +3 flaming. If he were to then grab a masterwork longsword, it would also get the +3 flaming enchantment. On the other hand, if he's imprisoned and, in the ensuring jailbreak, can't get much better then a common axe, it's just an unenchanted normal axe.
PCs who want to have a variety of different types of weapons can, now. The master of arms can have a short sword, and axe, and a javelin armed. Likewise, the young post-farmer boy wielding his father's sword has no reason to get rid of it. Fighter types are no longer depending on their weapon - rather, they're strong because
they're strong, though normal, shoddily built weapons can't let them really show it. Lastly, magic weapons stand out - there's no "Ho hum, another +1 weapon, throw in the bag with the rest," now when a magic item is found, it's rare and awesome.
I haven't had much issue with balance yet - keep in mind I'm doing this in a Pathfinder game that allows for most 3x content to be brought in, though I glare at a few caster stuff and books - as martial classes didn't really need to be balanced downward, and crafting time didn't balance much anyways.