But I guess the real problem isn't whether the patents usually involved will hold up in court, but the costs involved in setting up a defense and disproving the accusations.
I'm of the opinion that two measures will help fix the patent system, and this applies to most fields.
First, the duration of patents needs to be cut. 5 or so years would probably suffice.
Second, there needs to be an incentivized prior art busting effort. Perhaps the party filing the patent could put $1000 or so into escrow for a 1 month waiting period, and if someone manages to find valid prior art, they get the money.
Another thing that could help a lot is minimizing the extent to which patents can be sold. One of the biggest problems with the patent system that I see is that someone can invent something that sounds worthless, sell the patent for $10,000, and then the company that buys the patent can rake in millions in royalties. In general no one should be making money hand over fist for things that they neither invented nor produce.
How about: more than 50% of your employees are lawyers, or the lawyers in your organization make more than 50% of the money (to prevent a few lawyers from "hiring" a dozen or so highschoolers at minimum wage.
Patents should protect engineers, not lawyers.