USPTO is underfunded?
Bollocks. Just up the amount they charge to examine a patent so that it actually reflects the fucking cost of PROPERLY EXAMINING the patent.
Goddamn morons.
As for Software Patents specifically, either:
a) get rid of them, or for patents more generally
b) implement some kind of proportionality arrangement where the length and maximum monetary benefit you get from a patent claim is directly proportional to the effort required to develop the claim.
For example, pharmaceutical patents that require real R&D get protected as they still do today.
Patenting rounded corners on a phone gets protection for about 1 month, with a maximum benefit of $0.01 per unit (in other words, you'd spend more on patent attorneys than you would gain from the patent claim).