Currently, patents have worth well in excess of the application cost. Much of this is because patents are generally presumed valid - it's bloody hard to get a court to overturn one, for example. The article points out that this presumption is ill founded - patent examiners don't have time to do a thorough review - and suggests that the solution is to make it much easier to challenge them in court.

You want to talk about a situation where only those with money can make money? Make it easy to overturn a patent by hiring more lawyers. Cost of keeping a patent will skyrocket, value of obtaining a patent will plummet.

If you're going to have software patents, it seems much better for everyone to have strong patents by weeding out lousy patents before they are granted than by inviting constant multi million dollar legal battles.