It’s nice to have options when prototyping or just messing around. Over the years I’ve collected dozens of wall warts that work long after whatever they were originally for died. Many of these are not 5V, but are usable on FEZ (and other) boards. It is a “nice option” to be able to use these as an alternative to a USB power source. I agree that the mini USB connectors are almost as ubiquitous these days, but they just don’t stand up to abuse like a barrel jack. I’ve known several folks who had to get a new cell phone just because they were not careful and busted the USB charging jack. My personal painful example of this problem: my 6 year old attempted to plug in a wired xbox 360 controller “cause he saw dad do it”, bent the contacts, and shorted out the console! The red ring of death had me freaked, but I was luckily able to correct the short and revive my Xbox. Try shorting a barrel jack! It is much harder.
The connector does occasionally bump up against a shield so it doesn’t sit quite parallel with the FEZ. This may or may not be a problem depending on what the shield has for parts in that corner. I could see getting rid of it if you needed very narrow clearance in some enclosure. This would also assumes removing the pin headers for the same reason.
 As others have mentioned, having enough current is important. 5V/500mA just ain’t enough sometimes. I’ve used some sturdy 2pin JST connectors on other boards that were rated for plenty of juice. My vote - design the board to have a couple of options, and leave the soldering up to the customer.