It was my understanding that if you have a patent or own copyright on something, then unless you actively protect it you will lose it - for example, let's say a company makes a product that infringes on patents that you hold and you like the company so you ignore it, another company later on makes a product that infringes on your patent and you don't like that company as much - so you sue them. The company that you are suing can quite rightly point to other companies that are infringing on the same patent and question why they haven't been sued.
Now - back to the case in hand, when the alleged copying took place, Sun owned Java and any patents and copyrights therein. Even if there were discussions internally in both Sun and Google about the legal standpoint of the Android project, publicly Sun championed the Android project. It is only since another company bought out Sun - a company that had absolutely no part in the development of Android or any partnerships between Sun and Google - that it got upset and decided to go after Google. The fact that the then CEO of Sun has stood up in court saying Google has done nothing wrong (from a legal standpoint at least) is quite important.
If Oracle do in fact get away this - then there is nothing stopping any company from buying another company that created some software, and then suing anyone who made different implementations of that software, by claiming that the hooks that the alternative software uses are in fact copyrighted.
This can be thought of like a landowner, who for generations has not bothered about the fact that people go for a walk through some woods on their land, and actively help maintain the wildlife on the land - putting up bird boxes and things like that. One day - someone else purchases the land and implements an immediate ban on anyone accessing the land. Legally - they are quite entitled to do so (provided nothing has been written into the deeds stating otherwise). Morally - they are a dick.
This could all of been avoided if Sun had a written document that basically stated that they were OK with the way Google had used their code. But back when Sun was sold - the idea of suing anyone anywhere for the slightest thing - no matter how unlikely it might be that you would win - was not quite as common and depressingly frequent as it now appears to be.
As for fair use - well in music we are allowed to use 8 seconds of a song right? Given an average song length of 3 and a half minutes, I make that 3.8% of the total work. So - if it is alleged that Google stole 11,000 lines of code, can we simply say right - the total number of lines in the work is X million lines, and work out how many lines 3.8% would be. If it is less than the alleged theft - then Google is in the wrong, and if it is more than the alleged theft, then it's considered fair use?