We're talking in the context of a court case involving two enormous multinational corporations going at it for over a year and a half with probably another half-year to go, minimum. The "little guy" can't even afford to sit in the bleachers of this fight. If some "little guy" actually had filed these patents he'd have been bankrupt a year ago.
There's probably a patent regime that actually would protect "the little guy" but it's long past time to let the USPTO wear that fig leaf over the current system. (Which is to say, I'm not saying you're wrong, I'm more saying, your point is inapplicable. And that's a shame.)
I don't think there is any basis for your assertion that patents don't protect the little guy. I worked for two small companies that had, used, and licensed patents on their key technologies. These technologies took us millions of dollars and years to develop, and were our way of competing with companies that could out-manufacture us, but not beat us at the R&D game.
If you had to pay up front on the "value" of the idea, a little guy (be it a solo person or small company) could never file a truly novel patent. That would be even worse than the system now where you could patent it but not afford to litigate (but you would be able to sell it or if it's a great case find someone to take it on contingency).
In my mind, the little guy would patent with a small declared value - so on the downside they wouldn't be able to litigate for large amounts. But they would have a defensive patent, and that patent would also have value for larger acquiring companies because if they believed in the validity of the patent they could apply for revaluing at higher price (at which point there would be extra funding to make sure it is valid).
Yes, while it's low-valued it's not much of a deterrent to big players which is a disadvantage (depending on how often small players realistically can afford to challenge the big players legally under current system).
But by defensive usage I mean then at least you know someone else isn't going to patent your key stuff.
And once you've got funding/get acquired, the patent could be declared as higher value (and additional fees paid/validation done), and then future litigation to anyone who infringed after that date could be for higher amount.
There's probably a patent regime that actually would protect "the little guy" but it's long past time to let the USPTO wear that fig leaf over the current system. (Which is to say, I'm not saying you're wrong, I'm more saying, your point is inapplicable. And that's a shame.)