1. Get rid of the "presumption of validity". Patents, once issued, are assumed to be valid unless proved otherwise, but actually doing the legwork on every single patent to make sure it's good before approving just isn't feasable, so lots of bogus patents get passed.
But courts still defer to the patent office unless the case is unambiguously bogus.
Move to something more like the copyright system, where having a copyright issued only proves that you had a claim as of a certain date and that your paperwork was in order.
The burden of proof would then be shifted to the patent holder to prove that their patent was valid as part of an infringement lawsuit, back where it belongs.
2. Get rid of or at least weaken submarine patents. The obvious way to do this is to make it so that no damages can be collected for actions before the patent holder files an infringement lawsuit.