To the question of the Magicke Shoppe, I read an interesting article on that concept just the other day, posing the question of what we do in that "low magic realistic game" where magic is not a commodity. The writer suggested that, ironically, the only practical answer is MORE magical loot being found. Why?
Because the stats of higher CR creatures presumes the ability of PC's to pick and choose their magic items. If they cannot, they are de-powered. The PC who can purchase magic can walk his +3 weapon, with which he is an expert, into the Magicke Shoppe and power it up to +4. The PC who cannot will still need that +4 weapon to be as powerful as the stats of his opponents assume, but will have to find it, which means he will also still have the +3, +2 and +1 versions. That will mean his wealth per level is much higher than the rules would suggest, because it is largely held in items whose utility is overridden by his more powerful weapons.
The alternative is either downgrading all the opposition, or redetermining their appropriate CR in light of the PC's reduced power. Not a practical task for most GM's, and definitely an arduous and tedious one for even those possessing the needed skills and judgement.
