The lack of an independent invention defense (or some variation of this) is pretty much 80% of what's wrong with patent law in my opinion. A sampling of the issues an independent invention addresses:
* Obviousness. Patents are required to be non-obvious to a "person holding ordinary skill in the art", but obviousness is highly subjective and difficult to assess (especially for a non-technical jury). In contrast, evaluating whether something was independently invented, while not necessarily simple, is a more objective test.
* Utility. One of the rationales behind the patent system is that we want to encourage inventors to share their ideas with the world instead of just keeping them secret for as long as possible. While the patent system requires publication of the invention, it doesn't require publication in a manner that's particularly useful. If you could only assert patents against people actually using them, then you would have a strong incentive to make them useful (e.g. source code).
* Supply and Demand. The current system grants a flat 20 years to each patented invention, regardless of how difficult or expensive it was to invent. Recognizing independent invention creates the opportunity for a more flexible system. Inventions that are hard to reproduce independently are more valuable to society and should enjoy a longer term than easier ones.
The obvious problem with all of the above of course is how feasible it is to assess whether something was invented "independently". I've addressed that to some degree in this blog post (http://www.techdirt.com/articles/20121011/14171220681/yes-in...), but I admit it's a hard problem.
EDIT: Typos