Why would a business ever consider funding hundreds of thousands of dollars to research and develop a new product/concept, if any competitor could simply reverse engineer it, then sell cheaper since they did not have to recoup the R&D costs???
Consider the Blackberry case. Ultimately the patent was thrown out but due to an absurdity in the law Blackberry was held liable for damages (100s of millions) during the time before the patent was invalidated. Why should they have to pay for violating an invalid patent? If you were in jail solely for violating a law that was then found to be unconstitutional wouldn't you expect to be freed without completing your sentence?
Consider also
this case where a hobbyist releases a program then a corporation applies for a patent and sues him for $203,000 in damages. How could he be in violation of the patent when he wrote the program before they applied for the patent?
Another one to consider is Rhambus. They were part of a group to establish memory standards for PCs. As things were brought up in meetings they applied for patents and broadened the scope of patents already applied for. When the rules of the group were changed to require you to reveal any relevant patents that you owned or had applied for they left the group - then sued corporations for infringing those patents when the standard was implemented.
Then there is SCO vs IBM (just ended the 3rd year of discovery) where only now is IBM getting the specifics of what exact SCO Group intellectual property they have allegedly violated. (They have applied to have 198 out of 294 claims thrown out as too vague and too late for IBM to be able to know what SCO is talking about and build a defense case against before the actual trial begins). Why can the SCO Group get IBM to turn over evidence for 3 years without even telling exactly what IBM is alleged to have done?! SCOs reason is that IBM knows what they did so SCO doesn't have to tell them. Sort of if I accuse you of committing a murder and you have to build a defense and alibi without knowing who, when, where and how you are supposed to have committed the murder.
I think that the US Patent office needs to establish a fee schedule where patents rejected cost more than patents accepted to discourage applications that should not have been made in the first place (and encourage rejections of course). They also need to narrow them down and require a demonstration of a working prototype or at least complete blueprints. Finally automatic sanctions against any patent lawyer who was involved in getting a patent approved that was obviously not valid.