Wait times are not an accurate measure of an attraction's popularity. Wait times are an excellent measure of how efficient an attraction is. You would not say that Pirates of the Caribbean, which features 6 row behemoths of ride vehicles and a 15 minute ride length, is unpopular simply because its wait times only go above 20 minutes when the park is very busy.
If we were using wait times as a measure of the popularity of an attraction, then Finding Nemo Submarine Voyage should be considered one of the most popular attractions in the park thanks to its 30-60 minute waits at all times of day, even though the number of people in line/inside the attraction pales in comparison to a much more efficient attraction like GOTG:MB. Other attractions also have the same problem, where inefficiency leads to long lines; see Astro Orbitor (long periods of waiting between cycles leading to consistent 30+ min waits) or Storybookland Canal Boats (horribly inefficient loading means 20-30 min waits on low attendance days).
With its 6 loading areas sending 19 Guests every 2.5 mins or so, GOTG:MB is one of the most efficient attractions at the Resort (when each shaft is working, of course). It shouldn't be penalized for its sometimes smaller wait times just because it's efficient.
