That is not the problem. Just because an agency is funded by fees does not mean that it has perverse incentives nor corruption (though it can be the case). After all, the FDA has to assess all of Pfizer's drug applications -- do you want to pay for all that out of your income tax, or should Pfizer be paying it? Furthermore, the USPTO has had the same issues described here long before they were self-funded by congress.

The problem is that that the USPTO doesn't have enough money to hire inspectors and officials. They are woefully, desperately underfunded. The same problems that plague the USPTO also plague the IRS, and for the same reason. The USPTO would do much better if they were permitted to double the fees, or more, for patent application.