I don't think you can "craft" it up to masterwork after, only "magic" it up.
http://paizo.com/pathfinderRPG/prd/equipment.html#_masterwork-weapons
Missed that on my quick look at Craft - I was looking as it was the 3e rule. The sword itself is so trivial that making a new one once MW is a viable option seems less of a big deal.
Exactly. That was my point. Why even have the roll if there's no risk, or the risk will never be taken? Just set limits on what can and can't be accomplished, time and cost. Hence my suggestion to enforce caster level requirements (and the appropriate adjustments to items as needed to fit that).
Or maintain the current caster level, with the expectation that CL - 5, +5 for each missing prerequisite = spellcraft roll required to Take 10.
Under your system, would prerequisites be eliminated (opening up the ability to craft), would the caster need to be higher level to make up for missing prerequisites (moving items much more out of reach for a missing spell, say, or simply for crafting while on the road and wanting access to the spell slots - providing a considerable Crafting advantage to spontaneous Crafters who have the right spells - and also adding the math back in), or would the prerequisites be an absolute requirement, rather than something whose absence makes crafting more difficult? I suppose we could move prerequisites to be "the perfect tools", so you get a +2 Caster Level if you have all the right spells, instead of a penalty if you don't.
A failed Handle Animal roll, at the appropriate time, can completely change an encounter due to the animal misbehaving or not otherwise understanding. Failed social skill checks can introduce entirely new plot elements. A failed spellcraft check while crafting magical items can result in the loss of gold, and perhaps a cursed item that can be rather easily identified.
And a failed Spellcraft check at the appropriate time can also result in changes. Just like a failed Handle Animal roll to train the animal only imposes a delay (and just like I expect most trainers Take 10 anyway), a failed spellcraft roll to craft an object isn't likely to come up or cause any issues.
When you dig down to the root of it, the magical item crafting feats basically allow one PC to exceed Wealth by Level by 25% (by the rules... I know a lot of GMs see WBL as a guideline). If that's all it really does, why roll at all? Heck, take 10 basically does that now... it's just that you need to sit and calculate the spell craft check first to see if you can craft the item with a take 10. Just enforce Caster Level instead and you get the same effect, but no math.
As noted above, I think that also means trashing prerequisites, or we're back to math. Or we could just remove the roll, caster level and prereqisites from the crafting process entirely - if you have the appropriate Craft feat, you can Craft the object, as long as you take the time and provide the gold. Or we make the process much like other Craft skills - maybe you roll vs DC (set by caster level) each day of crafting and margin of success determines your progress. Fail by too much, and you have to invest in some more materials.
There's plenty of options. Making it match mundane crafting skills has some appeal in that a higher skill roll means faster crafting, and in being consistent with the mundane Craft rules. The present system provides for a lot less rolling and mathing out times, though, although you still need to math out the time, and possibly the cost if you deviate from standard items.
Finally, how does the feat apply to only one PC? The other party members help me out when they can, so why would I not also craft items for them? Whether I charge them cost and donate my time, charge the full market rate and get paid for my time, or negotiate a split of the savings so we both win, depending on the character's mindset. Better gear for the warrior means better protection for me!
