Well, actually, the issue was never whether or not Microsoft could ship it's own version of the JRE. The issue was rather that Microsoft had extended the Java API with it's own functions. Developers had started to use those functions, making applications written for the Microsoft JRE not backward compatible to Sun's JRE, and was thus subverting the standard.
Sun used the court to assert it's ownership over the standard, and the court ruled that Microsoft could not extend the standard. Microsoft, finding itself unable to embrace and extend with the ostensible view to usurping ownership of Java, decided instead to build their own competing product. Hence the birth of C# and the common language runtime.
The issue around Google's use of the API for Android is very different. The article says that the argument was that the Java API's are "needed to write compatible code" and so should not be copyrightable. If you followed the court case, you would know that the actual argument was that API's are not works of art, but rather a way to define a standard interface, and since copyright law covers works of art, API's should not be subject to copyright law. There were also a bunch of patents covered in the same court case, but these were ruled out relatively early on- with the exception of the rangecheck() function which was debated to death.
Android API makes no attempt to sell itself as a language suitable for back-porting apps to Java. Google did not copy Oracles implementation code for the Java API's, but does copy some of the Java API (definition, or application interface) code.
Android apps are initially compiled to Java ByteCode, but upon installation the Java Bytecode is compiled to another instruction format suitable for the Dalvik VM. There was another big hoo hah raised about Google copying the byte code, until it was realised that every Java developer on the planet does this too.
Google literally used the existing Java ecosystem as a working base, giving them a language and a compiler that produced Java Bytecode. They then built an installer that compiles Java Bytecode to their own Dalvic VM code format, and added a bunch of Android-specific libraries and API's on top if that. Oracle feel that although Java was made free by Sun, that there is "free", and then there is "free". They want their slice of the pie, and perhaps even deserve it. However, one gets the feeling that they may have had more luck by approaching Google directly with some sort of Java support contract than going to the courts on this one.