One of the reasons why I prefer the Skyliner is because the seats recline and you can rotate them to face either way. The standard seats on the JR Narita Express don't recline or rotate. I wouldn't usually be too bothered about the seats but the Narita Express is incredibly slow. As it uses JR's train tracks used by other trains, the Narita Express trends to stop a lot to wait for the other trains to get out of the way.
The Skyliner has its own track so its a non stop ride to Narita. I remember taking the Narita Express from Narita once and it took me over 3.5 hours to get back to Tokyo after a long flight - was miffed!
Delays, uncomfortable seats and an extra
1000 yen does not seem like a good deal to me so have avoided the Narita Express for all these years - things may have changed though.