Here's what I'd go with for crafting: it's extremely costly, but it's the only way to give your power to somebody else. Honestly, I don't want players crafting magical items as a matter of course; it might come up occasionally, but most campaigns (in my experience) don't have that kind of downtime, and even if they do, Trader Elminster's Magic Emporium is probably not the game you're trying to play. As far as characters making their OWN magic items, I'm happy to let them add special abilities like "Your sword is on fire" or "Your pants make you immune to mind-affecting effects" in the same way that their badassitude lets them add things like "Your sword is extra good at cutting things", by which I mean from the same reserve of Spirit Points or what have you. Have actual magic items stack with the "You are super badass" item effects (means your party still gets happy at finding a +1 sword, even at level 20, if they're all using base masterwork swords).
For actual crafting, maybe have a permanent XP penalty (not, "You lose this much XP" but, "For the purposes of determining your level, your XP total is treated as X lower than it really is; you still gain XP as if you were at the normal level for your actual XP total"). Definitely have a permanent Spirit Point cost, but maybe one that is numerically slightly less than the standard item. Maybe a permanent Con penalty, applied after all other effects, which can reduce you to 0. Stuff you're not allowed to fix, and which matters (the XP cost isn't great for this, since it basically just says "You can craft this many items without worrying"). If you want to be nice, have all the penalties vanish if the item is ever destroyed, and if you want an interesting dynamic have the items cease to function if the creator dies (unless there's some special component or other, typically something requiring a quest to get; this is tough to do while retaining verisimilitude, though, because somebody will inevitably try to set up a town and mine whatever it is).
A PC probably won't do it because the costs for themselves are greater than the benefits, and an adventuring group is small enough and ideally evenly powerful enough that redistributing magical power isn't going to be a tactical benefit; an NPC might do it occasionally, whether because they're a Court Mage who is able to leave a cushy lifestyle in exchange for keeping the Elite Guard magically outfitted, or because an Evil Empire enslaves its mages to graft their life essences onto magical superweapons, or whatever. Stuff that, unless the PCs are running a government, they aren't really going to be doing because they have to go on adventures and thus need those resources for their own personal stuff. Obvious metarequirement is that, regardless of the frequency of casters in adventuring parties, mages are a rare demographic overall, or else the whole thing falls apart again because there's no meaningful limit on how common magic is. This kind of the same paradigm that seems to exist right now in terms of PC versus NPC crafting, only taken to a greater extreme because the current one only works in Eberron, and even there it's not carried to its logical conclusion.
I never did get a fix for consumables, exactly. The best I came up with was that using a consumable returned its spirit points, but investing spirit points took Significant Downtime, like a 24 hour thing or something. Not really ideal.
All the above rambling probably has significant problems that I haven't noticed, and have probably actually been addressed in the thread, and which I'm forgetting about.
