I would look for unique features, a bottle opener somewhere at easy height. What really makes a good custom frame is a frame that meets the customers expectations, same thing a good production frame does.
I owned a "really good custom frame" that was built in the early 80's for 27" wheels. It was gorgeous, nice lugs, special front rack w. frame for holding removable front bag. Made out of 531 with appropriate geometry. Only problem is that it had a heinous shimmy above 25mph that required clamping the top tube with my knees. Next custom frame was built for 26" wheels and more road like geometry. Basically a sport-touring bike with super sturdy rear triangle. Except it really couldn't take a lot of rear weight without shimmying. Fast forward another decade and I've got a 26" wheeled Surly LHT, best so far.
I"ve known a couple first time frame builders who built a few defective frames that failed in races so I'd suggest whatever you get made you ride the hell out of it loaded up before you set out on a trip.