Roy's skin tone was lightened a few shades after the art upgrade. Word of the Giant says it's so he'll appear better when the books are printed. Same thing with Zz'dtri.
For a few hundred pages, Elan has been cosplaying as Locke from Final Fantasy VI minus the wig and bandanna. To be exact, he dressed up as Locke (and Thog donned a Moogle suit) to sneak aboard the Blackjack, then gave himself away, got thrown out of the airship, and never changed back. The new costume's a large improvement, though.
Schedule Slip: Early in the comic's run, the author kept up a fairly regular Monday-Wednesday-Friday schedule. Health issues eventually made this impossible to keep up on a regular basis, and he experimented with other schedules before finally giving up and making the official schedule "Updates at random". By the time this happened he was already one of the biggest names in webcomics and his site received more traffic than Marvel's, so it hasn't hurt his fanbase.
Series Hiatus: Starting September 2012, the comic was in an enforced hiatus after Burlew seriously injured his drawing hand in an accident. Updates didn't resume until the end of 2012.