I'm going to have to argue with you about this one -- you're comparing apples and oranges. Let's be fair here, if you're going to try to compare a 'naked' fighter to a wizard, then you'd best compare it to a 'naked' wizard.
Spell components: If you have a naked wizard/sorc/cleric that caster is very much screwed for the vast majority of his/her spells. Unless the caster happens to have the eschew materials feat (not bloodly likely) and uses it, the caster cannot cast the vast majority of his/her spells. If a fighter is stripped of all weapons, it's fairly easy for him/her to pick up any old thing and defend him/herself (heck, even a table leg!). On the other hand, strip a caster of his/her posessions and ask him/her to defend his/herself?!? You've got to be kidding! How common do you think those spell components are?? It's nice to see that in your campaign world amber rods (for lightning bolt) grow on trees, nevermind the (iirc) 200gp worth of diamond dust required for stoneskin (one of your own example spells).
The spellbook: Granted, this only applies to wizards but it's a very real issue. Let's say that the party of adventurers gets captured, stripped of all posessions, and teleported to the other side of the planet to a prison camp. This is a very real posibility for the 'naked' character scenario we're discussing. Now, should the characters try to break out. Odds are, the casters aren't going to be much help (see the spell component discussion) but the fighters/warriors/rogues will be able to use every skill/feat that they have (with a few exceptions like the weapon specific stuff). So, you have a warrior who may not be as well defended as he/she is used to. But, can quite possibly be quite effective as a break-out-of-jail tool.
Now, fastforward. Suppose that the characters actually break out of the prison. It's fairly safe to say, that recovering their stolen belongings isn't going to happen any time soon. So, the characters need to re-equip somehow. Well, the fighters and warrior-types can probably scavange some older weapons/armors off of some local brigands. The cleric might be able to scrounge up a holy symbol and some spell components -- with a little work. Similarly, the sorc might be able to find some of his/her required spell components. The wizard, on the other hand, is quite frankly fubared! He has to replace his spellbook!! Are you aware that a first level spellbook costs almost 2000gp to replace, assuming that you're given the spells for free (this is just the scribing costs). Try to imagine what it would cost for an L20+ wizard to replace his/her stolen spellbooks... Even creating a new spellbook with one spell of every level is a _huge_ investment for someone with no starting capital.
In short, please don't compare 'naked' any-class to 'naked' any-other class unless you take everything into consideration. Quite simply, any class would die if stripped of all belongings and sent against a demon/devil/dragon/etc -- some just might last a little longer, and some might actually hurt the thing...
-Eraslin