From my impression from being there last week, I think the longer lines are only partially attributable to popularity. The other part is due to how they are loading.
Capacity on the rides is severely limited. In the case of SDD, while the long was one of the longest of all our days, they were running about every third or fourth train completely empty (due to cleaning it and having to run it through once to dry off). And for the trains that were loaded with people they were at MOST half full, and in a couple of cases, we actually only saw one or two people on a given train (I couldn’t figure out why this was the case, actually).
Personally, I think they could have improved capacity a bit to get the lines down further. I think the need to spray down the trains every few runs was massive overkill. Personally, I don’t think they need to do it at all…that is what all the hand sanitizer is supposed to be for. Of course, unlike Universal, Disney is only making hand sanitizer use optional. At Universal, you HAVE to apply sanitizer before they let you on (since they actually squirt it into your hand just before you board!).
Anyhow, Splash Mountain is harder for them to improve capacity. Basically, it comes to a max of 1 to 2 parties per boat, based on the spacing they are doing. As such, capacity is severely limited. If they had a way to fill the boats, I think the ride would end up being close to a walk-on.
Omnimover-style rides fared the best because they really didn’t have to reduce capacity at all. It is no surprise that PhilharMagic, Muppet Vision 3D, and presumably Carousel of Progress (which is strangely missing from this list) would rank towards the bottom of this list, with INCREASED waits since the theater capacity in those cases was 1/4 the norm.
Space Mountain was able to reduce wait times a LOT compared to other coasters because the small capacity of each train being already quite small (6 people), it meant more people could still get on without wasting a lot of seats. Most trains, from what I could see, would have at most 1 to 2 people missing from the max capacity of 6 people. So, the lower crowds and the fact that it was running close to capacity with both sides open made a big difference compared to SDD, which resulted in a far more significant loss of capacity due to the longer trains.