I think the problem is that magic is simply too easy & too powerful in most games. It's more like super powers in a comic book or video game than stuff from myth or legend.
"They are that good" is fine & dandy, but the easiest answers are to be found by things like: rearranging spells by levels, reducing the number of spells possible per day/time period, making magic costly, making magic inefficient (or less so) in combat, etc.
If casting a spell takes a full combat round or longer, spells are going to be much more limited. Teleportation is pretty awesome even if it takes 10 minutes to cast, but it's a whole other animal than D&D teleport spells, let alone swift action teleports ala nightcrawler. Spells, not super powers (unless the genre IS superheros, then by all means have 3.5e style magic).
Flight, at least without an item or shapechanging into a bird, is pretty rare in myth/fantasy. Fly &/or overland flight could be tossed outright, or else made higher level spells (6 & 8 perhaps).
D&D spells are way too easy, too versatile, usable too often, etc. They always have been a problem, but d20 kicked them into orbit.
Just a few examples there, but magic/spells are the easiest thing in the world to "bring down to earth". I believe one is better off designing a game with that in mind, rather than boosting non-magic types up to anime or comic book proportions by default. The problem with "ordinary" folks leaping tall buildings, running faster than a speeding bullet, walking on water or flying, etc, is a complete loss of verisimilitude that kills many genres (not that genres with such expectations are bad, but they ought not be considered universal). I'm not saying to make casters unplayable, either, but toning them down is a better answer by far, IMHO.