hokiefyd 

They do. In particular, and especially with quick release axles, it can be difficult to get the exact same caliper alignment after a wheel change. I commonly tweak the caliper adjustment a little after a wheel re-install to get rid of some light pad scraping. Thru-axles are supposed to mostly eliminate that. It's a trade-off I'm happy to make, though. The biggest issue I have with rim brakes is squealing with moisture. I keep my bikes in my conditioned basement, and I wheel them out the back door (a walk-out basement) when I go for a ride. With the humidity during the summer time, my bikes will immediately "sweat" a little bit (cold frame out in hot humid air), and this causes issues with rim brakes. They'll squeal pretty loud for a little while, as moisture tends to do with rim brakes. This is not easy to "dial out", and is not an issue if I store it in the garage and ride it the next day.

First world problems, right?