It's worth noting that the Supreme Court has generally given rulings that suggest that intimate that software patents are broadly unpatentable. The key decision that allowed software patents in the first place was State St., which was never heard by the Supreme Court (indeed, in Bilski, every opinion went out of their way to emphasize just how wrong State St. was).

Between Bilski, Alice, and even the older decisions of Benson, Flook, and Diamond v. Diehr, SCOTUS has generally held that most software patents are basically inherently invalid. It should also be pointed out that many patents favored by trolls would also fail obviousness and/or prior art tests: the problem isn't that the patents are valid, it's that trolls can extract money from people by charging them somewhat less than the cost to go to court to prove that the troll's patents are invalid.

One way you could fix the system is to punish the trolls for knowingly peddling invalid patents: if an entity gets three patents invalidated by the court system and they've been aggressive in suing people for compliance with those invalid patents, then all patents that they hold are summarily invalidated and they get prohibited from enforcing any patents for 5 years. On top of having to reimburse everyone they charged (plus damages… plus interest ☺).