Spud,
You raise a very valid point, one that I think you've already answered. Fenders are commonly accepted as bolt-on only, and Gibbys are set neck only. As you've mentioned, I've noticed a number of set neck Fenders over the past few years that seemed to fail miserably. The one that I played (a strat) seemed to be a very solid, playable guitar. But the fact is, no one is willing to believe or accept that Fender can produce a quality set neck guitar. The same holds true with Gibson. If they switched all their Les Pauls to bolt on construction, regardless of quailty, two things would happen. The first, would be a serious plummet in sales accompanied by a hailstorm of public complaining. The second would be a dramatic spike in the value of set neck Lesters on the secondary market.
I guess it all boils down to what we've all grown comfortable with. Another good example of this is the SG Supreme (and the upcoming SG Prophecy line). To a purist, these are SG's in name only. The change to the scale alone makes them dramatically different from any other SG on the market. They're still great guitars, but they don't seem to do as well as the more traditional models.