I've put a lot of work into trying to limit magic and give magic a sort of scientific or logic behind it.
First, magic is split into two forces, Divine and Arcane. Divine loosely defined as the magic of Gods or the will of the Cosmos. Basically its like Arcane magic but seems to possess its own independent intelligence. As if it were part of some greater intelligent entity or entities. Arcane magic is raw, chaotic and unstable in its pure forms.
I've put a lot of limits to magic, in fact Yanagi's list is pretty much like my list, however I have a few additions...
Unknown spells: Some spells in the litany of splatbooks, the SRD and elsewhere may not actually be known. Basically I know create water is in the SRD, but that doesn't mean my setting has such a spell available. Other spells like say "Fly" for example are plausible but have not been invented. So no spellcaster has figured out how to use magic to grant flight. Or if any have they died before they could teach it or write it down in a way that others could learn it. In terms of Arcane sciences, its still a work in progress and people are still researching how to manipulate this curious "force," in nature.
Magical Instability: My setting has all sorts of things that limit Arcane and Divine magic. For Arcane magic it is the simple fact that over time some spells decay. Even spells cast with permanency may fade over time, or be altered by the latent magic of the planet. Some areas of the world have dampened magic, in fact the geology of the planet can effect spells... especially a high level spell, one that's permanent ect. Divine magic has the effect of being effectively its own intelligence. The intelligence that is Divine magic can chose to rescind the spell at any time.
Basically magical means of doing things either aren't available or are simply too unstable or haven't been mastered.