I am currently looking for a lawyer to help me figure some of this out. There is a flip side to this problem. If you become successful with your project, and did not do cretin legal filings, some one with bigger pockets can screw you. It happened with some model railroading software. An open source project got S&D letters and taken to court by a very large player that started using the opensource projects IP. The project won the lawsuit but it cost them several hundred thousand dollars to fight it. Had they filed the right paper work it would have been a rubber stamp with for MUCH less cost.
I'm not sure I agree that filing the paperwork in advance necessarily stops the bad guys. For those with deep pockets, such obstacles are typically mere speed bumps if the patent is valuable enough. Your only hope under the circumstances is to either sell the patent or right to an entity with even deeper pockets to to find a bloodthirsty law firm that is willing to lawyer on a contingency basis.
Patents and copyrights make excellent barriers to entry, hence the proliferation. Not only are they great means to control market entry by potential competitors but they also make great bargaining chips between companies. See the latest Apple/Moto agreement among others.
So. by all means file for protection and so on. But recognize that you can be sued for anything in the US, a process that has been used by the government, corporations, the wealthy, and cults alike (ie SLAPP) to attempt to silence critics. The only remedy I can think of would be to require loser pays rules as in Europe. That also has benefits as far as reigning in frivolous law suits. However, what do you think the chances of such radical change are passing in congress where over 95% of all members are lawyers? They like the system as it is because it assures a steady stream of work.
I did not say it would stop the bad guys but it DOES help with your defense. It is simple insurance that may or may not help, depending on the circumstances. But if it helps it will help BIG time. If it does not help the original cost will just be a drop in the legal fee bucket any way. To me it is just due diligence if your trying to commercialize any thing.