I use an elliptical instead of a trainer for a couple reasons. One is that it's a full-body workout, so it really is easier to "compact" the length of the workout while doing an equivalent amount of cardio. The second is that I find the similarity between indoor and outdoor cycling causes me to go into the alert mode of brain activity (scanning for traffic, obstructions, etc.) I'm using on the road while I'm riding on the trainer. There's nothing more boring for me than to be super-conscious of what I'm doing while I'm actually not moving. It makes every hour seem like 3. I can zone out on the elliptical and watch tv or listen to a podcast on the elliptical, but I'm just not able to split my attention that way on the cycle.
I can't prove it, but I suspect that the elliptical is also a lot better for working out my knees.
The advantage of indoor cycling is the workout is closer to outdoor cycling, but as a general fitness machine, I don't think it has a lot of advantages over something that requires you to keep your body upright.