I have no problem swapping pickups, most of mine have non stock pups in them. Rios, Voodoos, some that I woulnd myself.... My Huber has Haussels in it like stock, except Haussel wound them to my specs for me.(Not that I'm a big shot or anything, I just had particular specs!!) Rarely does a company use versatile enough pickups to satisfy every ear, like restaurants rarely get all the spices right. That's why you see ketchup, steak sauce and other condiments readily at hand. Removing typical pickups from typical guitars does not hurt the value, but down the road, having the stock pickups can make a huge difference in the value of a guitar, whether they are in the case or hooked up. Do what works for YOU, you are the ultimate judge. Oh, and buy your pickups from ME, so I can feed my kids. LOL