Exactly. The Peter Pan ride is liked well enough by many, but the line is usually so long only because the low throughput of the ride system and its location right in the heart of Fantasyland.
Under the Sea - Journey of the Little Mermaid probably has an hourly ride capacity around 3 times that of Peter Pan. If you magically swapped the locations and the hourly ride capacities of these 2 attractions, you would see the Little Mermaid would be the ride with a 90 minute wait and Peter Pan would have the 20 minute wait.