I agree completely. One of the key problems with software patents is the very idea that an algorithm is deemed worthy of patent protection simply because it is not obvious to the "average practitioner" of the art. But what skills/level of creativity constitute "average"? What if you have a company, like Google, whose core hiring principle is to find people who have above average skill and creativity? This seems to set up a perverse disincentive to hire smart people because the smarter they are, the more likely they are to rediscover on their own an idea that is already patented and thus violate it.

The fact is that if the idea patented truly is the best way of doing something then a lot of smart and above average developers are likely to unknowingly bump into that idea out of necessity. And this seems to be a problem that is unique to software patents precisely because of the closeness of software to mathematics itself. Some algorithms are provably optimal for a particular problem which means that everybody smart enough that faces that problem will solve it the same way. If you're smart enough to come up with the best way of doing something on your own but can not use it because it was patented then you're forced into a wasteful outlay of creativity just trying to work around the patent. I don't see this as spurring innovation or at least not worthwhile innovation.