We tried this. It led to the current insanity with software patents and software trolls. I also don't see any indication that innovation would stop if patents didn't exist (see: everything done in the Linux kernel). The trade-off is clear: patents do more harm than good. Get rid of them.
Independent inventors rarely seek patents and their best bet to contest the patent is to sell it to a patent troll, companies tell their employees to never read patent filings to not be willfully infringing and truly novel patented ideas are simply avoided until the patent expires or alternative methods are found (eg ECC crypto).
I'm sure you can find some cases where patents have served as a social good, but I expect them to be outweighed by all their negative outcomes.
It is used, because it is the only one widely compatible, especially with Windows.
If Windows supported F2FS for example, everyone would be happier.
But what would be a motivation for Microsoft to support a good, free filesystem? One, that it cannot ask a fees for?
Not to defend software patents, I still think they're a stupid idea, but for patents prior art applies to the exact workings of something, not the general idea and concept.