Sounds like a design problem.
You mention that these are faster than the old buses on hills and the highway.
This would indicate that these buses are optimized for improved performance with the same horsepower and fuel economy. Specify a smaller engine next time, and performance will drop to the level of the old buses, but fuel economy will increase.
Some of the new hybrid SUVs are being designed that way on purpose- to get more performance for the same fuel usage.
If you spec an engine large enough to maintain highway speeds on steep grades, then you have too much engine to really get the best advantage of the hybrid system. In fact, due to the added weight of the hybrid system, the vehicles will most likely get worse mileage running up and down hills at highway speeds.
And you noted that the maintenance savings are $3 million per year. That buys a LOT of diesel.
$44 million ($47 million - $3 million maintenance) buys a heck of a lot more....