The key to getting busses to spread back out during the day comes down to the difficult duty of managing chaos. Since the drivers are on a closed loop, it only takes a short delay for another vehicle on the same route to close the gap. From there, more people are left waiting at stops, which causes things to move even slower. The situation just keeps getting worse until you see a procession of public transportation coming down the road.
Using a simple game that you can try, the City Metric piece goes into detail about many of the factors that cause these frustrating delays. While it's possible to improve the situation, completely fixing the problem is largely impossible due to the way our roads work. Give the whole article a read to better understand why. The explanation unfortunately doesn't make waiting for a bus any easier.