Patents have some specific requirements before they are allowed. You can't just have an idea for something-- you have to "teach" the idea and "show enablement". Meaning you need to explain how to do it, and that the technologies exist to do it (faster than light motorcycles can't be part of your invention, for example).
Granted the patent office isn't perfect at screening these things out (see: perpetual motion) but you can't just say "I have an idea, pay me".
The problem is I can patent an idea.
I can patent something that says like "the invention is a computer that runs a software program and that software program does....".
Without the actual algorithm, I have patented an idea.
There is no way to work around that patent because it has encompassed every variation of algorithm, even though the original invention has none.
The patents in this case are applied incorrectly.
This company asserts that any communication like Skype or FaceTime is infringing no matter how implemented.
Apple doesn't even use the same mechanism. Their idea and implementation uses NAT and hides the IP address as a method of security. FaceTime doesn't work that way.
The other issue is the jury has no understanding of technology so you can effectively say enough junk and fool them.
Patent cases should be tried with a jury of people knowledgable of the topic.