Most judges and juries have no idea about technical details of say a program or a chip. So when Apple or someone else comes in challenging a competitors product, they will often rule for the more well known player rather than the new innovation.
Seen it in my field a few times.
So much so that we are very careful about what we patent. To often it becomes lawsuit bait from our competitors. They will sue just to stop the process, and drag it out long enough that it becomes to expensive to keep fighting.
So you might agree that it is not patents as such that are the problem but the procedural ability to abuse the system.