Just did the loop in June of '09 with one detour. GTS was not fully open, so we had to go around the edge of the park to the W. Glacier entrance. However, the following day we did get to ride up the west side to Logan Pass and back down again. (In ’99 I climbed the west side and descended the east side.) We started in Whitefish and went clockwise. I agree with Valygrl for the reasons she notes and others, including...
1. Leaving Waterton Village heading towards the U.S., the climbing on Chief Mountain Highway (MT 17) will be more forgiving. You will have climbing for sure, but it will be easier. (I have done it both directions.) The trade off is that you will almost certainly have a stiff headwind from the junction of MT 17 & U.S. 89 to St. Mary, but it's relatively flat.
2. West to East on GTS Road is also wider. Also...there is an ongoing rehab project, which I think is mostly on the west side. You may encounter unpaved sections depending on when you go. I prefer descending unpaved roads to climbing them. Check the park's official web site for details and potential road closures. The bike restrictions noted could be important. Going west to east, you must reach Logan Pass by 11 a.m. or risk a fine. East to west, you can ride the road between St. Mary, over Logan Pass to Sprague Creek Campground at any time. You cannot go west of Sprague Creek between 11 a.m. and 4 p.m. Sprague creek is a nice, small campground on the lake with $5 hiker/biker spots, and it's within walking distance of Lake McDonald Lodge (which also has a camp store and a bar that allows you to take drinks down to the lake), so it makes a great place to stop for the day.
3. There is an unpaved section between W. Glacier and Columbia Falls. (Follow the map's advice and take this route instead of U.S. 2.) It's predominantly downhill going clockwise, which should makes things easier.
Here is a link to some photos of our recent trip:http://www.flickr.com/photos/davez2007/sets/72157620763740044/
Send me a private message if you would like more details about what we encountered.