Comparing what you think should be an apple (EPCOT's Soarin') to another apple (DCA's Soarin' over California) seems like it should tell the story of why the wait times and therefore the popularity of one is different from the other; but, that simply doesn't tell the proper story and is more like an apple>orange comparison.
When you try to compare and contrast these two rides, you need to compare and contrast the parks they are located in. The issue at hand is not the individual attraction capacity (number of riders per hour per attraction) as they are the same (or close enough due to the single rider factor in Cali). The issue at hand is the attraction capacity the entire park can handle and does handle (number of attractions x the individual attraction capacity).
The Soarin' twins can be used as a case study to the REAL problem in Orlando in contrast to Anaheim - the number of attractions per park. It's the per park attraction capacity that is the heart of the Orlando problem. There simply aren't enough rides and attractions per park (esp attractions that guests want to visit) to steer guests clear of the "headliner" attractions at each location. Since TDO is too cheap to invest in increasing the number of attractions per park or at least "plussing" the attractions that people don't want to currently wait in line for (like Imagination or World of Energy), they've had to invent FP+ to try to steer guests to these attractions and away from rides like Soarin' by giving them a FastPass to an attraction like Imagination.
Soarin' at California Adventure doesn't have consistently long lines like EPCOT because its in a park that has 8.5 million guests last year vs. 11.2 million at EPCOT and more importantly - it's in a park that has Radiator Springs Racers, ToT, Screamin', Midway Mania, Mermaid, Aladdin, Grizzly River Run to pull guests away from it. In EPCOT, you've got... Test Track as a major draw and that's about it these days. That isn't a slight on SpaceShip Earth or anything; but, none of the EPCOT attractions have the same drawing power either in ride quality or more importantly "newness" to make a dent into Soarin's line.
Increasing EPCOT's Soarin's capacity per hour by adding another theater will help; but, it won't help the fact that the rest of EPCOT can't pull it's share of the weight.
The "problem" rides at WDW like Soarin' and Midway Mania are more of a testament to the lack of capacity at their respective parks than simply the hourly throughput of each ride. People line up like crazy for them simply because there isn't anything else they feel they would rather do at each place.