A couple of thoughts for the pro-skills camp:
Some of the spells that are commonly thought of as making skills irrelevant actually still involve a check. Exibit A: Knock. It doesn't automatically open locked doors.. you still need to make a caster level check against the Disable Device DC. You can more easily get bonuses to the skill check (morale, equipment, etc) than to the caster level check.
Another thing that often skews in favor of spells over skills is a loosely enforced equipment system. Yes, a scroll of fly or spider climb will render a skill check moot, but should the scroll or potion even still be intact after you were slimed, fireballed, dropped down a pit, or etc earlier in the adventure? Checking for damage to equipment is virtually never done when a PC fails a save vs some nasty fate, and remembering to do that can help reward skill investments.
Skills, unlike potions or scrolls, can't be sundered or stolen.
Skills, unlike spells, can't be turned off via Dispel Magic.