We have stayed at the Contemporary numerous times. My understanding is that the Junior suites are only available in the wings. Although we love the CR, we do think that it is night and day between the wings and the tower (especially facing the MK), the tower being far superior to the wings. Many people who have stayed at the CR and stayed in the wings have not liked it very much. The rooms in the tower just seem brighter. The view is magnificent, the atmosphere of the concourse/atrium with the monorail running through is cool. And the monorail seems like an elevator ride away. The wings just seem far from it all.
Our preference (ours only) is that if we can't stay in the tower, to go somewhere else. Having said that, the Junior Suites at the WL are a little cramped as well. If you can get a good deal on a tower room (based on AP rate or similar), have you checked the price of adjoining rooms in the tower? It may be comparable. to a suite (some of which AP rates don't apply for).
We are staying at the AKL lodge next week and the AP price of $120/room ($240 for 2 rooms) was the same as the $240 for a JS at Wilderness, (and also the same as a 1 bedroom suite at Boardwalk and 1 bedroom suite at YC BC). Ranking all those rooms the WL JS suite easily ranks last.
