I'm a huge fan of mahogany and rosewood (occasionally with a top). There aren't many options for mahogany on mahogany that are neck-thru or properly bolted on.
After a while, anything else sounds a bit off, to me- granted, I've owned, heard, and played some truly wonderful guitars that had nothing to do with mahogany or rosewood.
I don't particularly care about the upper frets, so the joint isn't terribly important.