Sections of lines that already have meaningful congestion at adjacent stops wouldn't be a good target for balancing. WMATA in D.C. recently eliminated about 5% of bus stops as part of their overhauled bus network, this is how they described their strategy[1]: "We thought carefully about each stop, looking at things like how many people use it, how far away it is from the next stops, and whether it's safe to walk there. We also listened to feedback from thousands of bus riders."

Additionally, many stops with a lot of people loading and unloading are hubs which would never be balanced away, and often are designated timing points where the bus will wait to get back on schedule, so loading/unloading time is often irrelevant because predictability is being prioritized over speed. Improving speed and consistency with techniques like removing unnecessary stops increases predictability and allows for tightening up timetables and minimizing average hold times.

[1] https://www.wmata.com/initiatives/plans/Better-Bus/frequentl...