at lease at POP there were two lines, one online check in, other was normal check in. We did online and were in and out, and on your way to the parks within 3 mins. I dont think the other line moved
I always have called and they put a note on my resv. about a room request. You can still request a room if what you get is not what you want at online check in.
I always do online check-in. I just think it is a lot quicker and easier and then line has always been shorter for me.