I've only been on the Glacier Express route from Chur to Disentis, and then only with the normal train service, but it's a pretty route through the 'Swiss Grand Canyon'. I often take visitors on the train from Ilanz down to Reichenau or Chur.

One big difference of the Glacier Express from the normal S-Bahns though the Rhein valley from Chur to Disentis is that the Glacier Express wagons have panorama wagons. The normal trains do not. The panorama wagons would be pretty nice in the canyon.

Though, if the weather is good, I'd probably go see the Matterhorn instead. If you have time, the trip up to the Klein Matterhorn is pretty nice, and you can walk on the glacier.