This community is focused on software patents as being special. They are of course, but not that special:
In a lot of other fields the patent system is way out of touch with the reality, too.
And secondly: What is wrong with patenting some genial algorithm over some drug? Both can be equally inventive.
We need to focus on what is wrong with the patent system in general:
1) Way too many trivial patents are issued.
Maybe the patent office should continue working like now, but then the sociaty and especialy the courts should realize that a patent is not a big inventions, but something which can easily - and very often will - fall in a an actual trial. Maybe the first time a patent is tried at court, it has to be reexamined with a much higher care than was done for issuing it. That way issuing patents will continue as now - i.e. things gets published - but evaluating the actual validity for litigation will be an expensive process, which comes later. A lot of patent holders might realize it is too expensive and drop it.
2) But patents like "using known technology X in Y" should not granted unless it is a non-trivial thing to do. Right now you can get patents for using a known technology in a new field without actually having invent anything in the process.
3) The patents themselves are unreadable. The patent database is supposed to be library of inventions for others to use, not merely a pile of unreadable stuff written by patent laywers. The inventions should be directly implementable from reading the patent.
4) The damages for business is way too high for using patented technology. That means businesses stops developing new stuff because they are afraid of litigation.
The damages payed should only be the value of the technology in the product, not some arbitrary theoretical number of how much money the patent holder have lost. If the patent holder will have to prove or at least argue for how much the technology is actually contributing to the product, a lot of the trivial (software) patents cases will go away, because the patent holder can only get a very small amount of damages.
Essential only "essential technology" in a product should be litigated: Using substance X in a drug is very essential for the product and needs to be protected. But using "swipe to unlock" is no essential and should therefore not be able to draw a lot of damages and therefore worth the efford of littigation.