Originally Posted by Miek
I like bolt-ons because I can shim the neck if necessary. I'm a little more wary of lower end neck-thrus (admittedly they're not that common so it's not a big deal) because there's no salvaging the neck angle if it's wonky.
This is how I feel too. I don't really consider the effect on the tone because there are so many other factors that you could easily negate the effects the neck joint would have. It all comes down to comfort/ease-of-repair/ease-of-setup for me.
That said I won't dismiss any guitar because of its neck joint type.