Its not really magic users, its magic gear.
Slippers of Spider Climbing really embody the problem. They grant a climb speed. Once that happens, it doesn't matter what your climb skill looks like, or what your armor penalty looks like. They completely negate that entire aspect of your character.
So you get in a weird situation. If you give them to the guy who likes to climb, they're redundant with his climb skill ranks. If you give them to someone who's terrible at climbing, he's significantly better than the guy who invested valuable skill ranks in climbing.
Spells can make a rogue's abilities obsolete, but at least they run out, or require the spellcaster to fill up spell slots with Knock instead of an attack spell. Its gear that creates the problem- a 50 charge Wand of Knock can last most parties a very, very long time, and isn't all that expensive. And Slippers of Spider Climb grant 10 minutes of climbing every day.
And that's not even getting into the ways that advanced magical tricks like flight and teleportation rain on the parade of classes based on mundane maneuverability.