Pickups

Pickups are really a huge factor. Most guitars now are built reasonably well - you can get good guitars for < $1000, or up to as much as you want to spend, but you can get a reasonably well made guitar for < $1000 now that will intonate correctly and sustain well, and the necks are pretty good to where you can get the action where it needs to be. Upgrading the pickups in one of these lower cost axes can make a HUGE difference in how it sounds. I've always had to swap pickups out. I never like the stock ones.