I don't mind it. Of course, having everything on one disc is better but it only takes a couple of seconds to swap out. On a couple of occasions, I've actually loaned out a disc while I played on the other disc (L.A. Noire, Metal Gear Solid on Gamecube) so it actually turned out to be a benefit.
Getting up to charge a controller, get something to eat, answer a phone, take a dump, or jiggle my Wii component cable (My cheap-o Wii component cables SUCK!) are about as annoying as changing a disc. I'd only complain if content was cut or the game is more expensive. SInce that's not the case, I'm cool with changing discs.