I have both bolt on and neck-thru on guitars and basses, and I personally prefer bolt on, simply because of the neck ever happens to need to be replaced for whatever reason, you can just get a new neck. If anything nasty happens to a neck on the neck-thru, it seems like the money you'd spend on a repair like that would be way more than you'd spend on a new guitar, plus it wouldn't be pretty, if it was even possible. From a tone standpoint, to be honest I haven't noticed much of a difference. People say there's a difference in the tonal qualities and maybe there is, but I guess it's so subtle that I just don't really notice it. So from a personal preference standpoint, for me its bolt on, but if I want an instrument, I'll take whatever it is either way. It's not a deciding factor for me, just a personal preference.