If you just put up the wires for part of the route, can't the bus charge up while it is under the wires for the rest of the route?

No, you bring back all the disadvantages I list - perhaps on a smaller scale but they still exist. You are still forcing all your buses to put part of their time on a pre-defined route. Maybe you can say we will always use this central station and put wires for a few blocks around it - but after that your buses should be spreading out in different directions. This isn't enough to get a significant charge.

It is an idea that seems sound, but fails because of reality.

This is exactly what they do in Shanghai and it works. The rails are not for the whole route just long stretches with lots of lights.

As far as I can tell they have a mixed fleet. Electric for ones that are downtown enough to charge and natural gas for busses that are mainly outside the city.

Things change rapidly so this may no longer be true.

Well they actually do this in Seattle and it seems to work out. A fixed route is also not a bad thing (see bus rapid transit) and can encourage private development.

See the last paragraph in my original. Fixed routes to have advantages, but only when/where you are sure they are very busy and will be for a long time. Most routes are not that sure in the modern world, so the flexibility advantages of non-fixed routes is important.

Of course part of the advantage of flexible routes is we assume car infrastructure is in place. While that isn't entirely desirable, it is reality: anyone fighting it directly is ignoring reality. Better to fight it indirectly which means making public transit better and better until people decide on their own to get rid of their car - only when few people use a car regularly can getting rid of roads be realistic.

Build it and they will come doesn't always work.

You can't ever really get rid of the roads, you can only downsize them. Even if everyone uses public transit, you need some way of transporting goods and cargo, and the only way currently of doing that within a municipality or to most final destinations is by truck. Whether you're moving a shipping container full of stuff to a retail store from the train terminal, or you're packing up someone's home and moving their furniture to a new apartment, it always goes by truck, and trucks need roads.

But if we could get rid of cars, we could make the roads a lot narrower.