I get your point, but wait times aren't really a great indicator of popularity. I'm sure someone with better knowledge could correct me, but my experience and impression have me thinking that River Adventure is a high capacity, fast throughput ride. If its waits on any given day are shorter than, say, Dudley Do Right's, does it mean that it's less popular or that it holds a lot more people per ride? I would argue that JPRA is still a premier and popular attraction, with great capacity, and worth keeping around.
Time will tell, but wait time shouldn't be the indicator. Seven Dwarfs Mine Train usually has some of the longest waits at Magic Kingdom, Peter Pan has long waits as well, but they're far from the most popular/famous rides in the park.