I'm not sure how to look at this statistically, but isn't the OP a counter-example?
>Make the application fees cover real research
Not really sure what you mean here. How much is time worth?
Okay, so I have an invention right now that I think is really novel, and I'd like to build a business around it. I may just want to patent and license though. Roughly speaking, it might fit roughly in the "Mathematica" space - note the example of an inventor (Wolfram) making good money on his (software) invention! Isn't that how the system is supposed to work?
Here's another question: of all the innovation in the internet space, what, if anything, do you think is patentable? Is the Facebook feed novel? If nothing is, doesn't this leave the only businesses the ones that are social, the same ones that treat users as product not customers?
The patent system is intended to allow for inventors to recoup investment and make money. It was started in a time where it would take literally years of R&D and a decade to even break even on hard, physical costs. Software and process ideas take minutes to come up with, and hours to develop... A single license/sale generally recovers any creative investment.
Design and process patents are ridiculous... most software patents are absurd. I work in software, and tbh, there's almost nothing I've seen in the past 20 years that doesn't specifically tie to a physical device in software that is deserving of patent protection, and even then not for 20 years.