What makes a durable and dependable commuter bicycle?
You probably have too high expectation. I imagine very few bikes with Sora quality components would be ridden that far in 10 years, let alone 1. 

With any bike the amount of regular maintenance is far more important to longevity than any other aspect. At those distances, a weekly maintenance check on the normal stuff - tire pressures, cleaning and shifting, brakes etc needs to also include tires, wheels and spoke tension, chain wear and bearings (Headset, BB) etc. 

Buying something like a Surly would be a good choice, any brand renowned for reliably rather than performance (Clydesdale vs thoroughbred) would be a good choice. Most main stream brands have a model that is aimed to be robust than their out and out racers, so its more matter of choosing the right frame, then the right component level. 

At those distances, 105 would be a good level to aim for. Too high spec components are trading durability for weight. Low spec will wear out too quickly. 

Wheels and spokes fail from poor initial build quality and lack of maintenance - a Sora quality bike would have come with machine built wheels so chances are the problems started before it left the factory. Upgraded wheels are better to the point they are being made lighter rather than stronger.  if you really want them to last, go for 36 spoke wheels, and get them tuned by a good wheel builder before riding, and after a few hundred kilometers. Wheel made for gravel or touring bikes will last longer than wheels made for speed.   

Crank failure is most likely due to something other than high use - accident damage or manufacturing fault. Cranks do have a very high margin of safety as a failure is catastrophic - More expensive cranks are usually stiffer and lighter, and if anything, weaker rather than stronger.