Nokie wrote:"maple necks sound brighter than rosewood necks" that in my experience has no basis in fact.
It does have basis, but it's part of such a huge "with all other factors being equal" cause-and-effect system of what affects sound and what doesn't, that it's virtually meaningless and people toss it around like some kind of basic rule.
However...for quite a few years I played a '65 jazzmaster with a pencil-thin neck that I couldn't stand so I put a great big U-profile maple Tele maple neck on it. How much of the difference in tone was the material, and how much was neck dimensions? Hard to say, really, but you could hear a difference - even acoustically.
As for the "depth of neck set" thing - think about it: the less contact area there is between a neck and body (and this applies to glued-in necks as well) the more free the neck remains to vibrate. The less rigid and inflexible the whole assembly is, the more it will absorb high frequencies (which your ear then interprets as a "rounder" or "warmer" tone). Now if you acoustically diminish the high end response of the guitar, that's where pick attack lives - highs and upper mids. When you make contact with the guitar string, you produce what is known as transients, once again these are in the higher registers so any dampening via the guitar will have a noticeable effect. This is why we think of hard materials such as maple as producing a "quick attack" - all the pick transients and harmonics jump right out instantly, as opposed to the "vocal-like" vowel-y sound of, say, an all-mahogany instrument.
Once again, like the maple vs rosewood thing, there isn't one single determining factor, the instrument's sound is a combination of many elements, and in the cases of wood some of them are quite unpredictable since you're dealing with an organic, variable-density material.
So what's the point of my "brief, reactionary" response? I hadn't realized that I was required to submit an epic-length post on the topic of vibration absorption in guitar designs. I was actually agreeing with you - YES changing pickups in a Strat won't make it sound like a Mosrite...I wasn't expecting to be given the 3d degree about it.