Bus routes are already subject to pretty sophisticated optimization. You can push utility around to do different segments of the community depending on your political priorities, but there aren't global optimizations just sitting on the table. Unless your transit agency is really incompetent, in which case you have to ask why your call to "improve the bus system" today will fare differently from all those that came before.
If that were possible, it should have already happened.
The bus just isn't going to take people point-to-point. It will go to a hub, and then people will change buses, and then another bus will go out. Point-to-point service is personal transportation. Shared transportation fundamentally can't be optimized to individual needs.
So the buses drive longer distances, and they have to drive even when empty.
BTW, bus usage can seem better than it really is. You are likely to go on the popular parts of the routes, so you see the buses being fuller than they usually are.