Nothing new here.
No doubt, this is a major disappointment since patents are responsible for just about all the ridiculous litigation for software developers, but it is not a surprise. The court merely confirmed what was already known, that software and algorithms are eligible for patenting in the US, judges cannot rewrite law from the bench.
Patents make the software field less competitive. They are an impediment to independent developers who cannot afford the increasing costs of patent protection and litigation, but who are otherwise very talented at contributing both commercial and open source software.
The entire system would collapse if it wasn't for the fact that most companies get by ignoring the patent system until they're sued at a time when they're more profitable.
It's impossible to develop modern software without infringement. There are simply too many developers working worldwide to track each invention. Even if this were possible, the notion that they wouldn't bother developing without patent protection is ludicrous.
Patent documents are written by and for lawyers, the benefit of having them published to disclose how they work is completely useless to the modern software engineer. Resources made available on the modern WWW are simply higher quality than patent documents ever could be.
Clearly the world would be better off without software & mathematical patents, but now that we have them, patent trolls feel entitled to them and they have the resources to ensure it stays that way.