The more plausible reason Apple doesn't sue Microsoft is their lack of success in the space. Windows Phone has negligible marketshare and almost certainly loses money given the huge upfront costs of building an operating system and software ecosystem. It'd be hard for Apple to claim they lost a significant amount of revenue or sales from Windows Phone IP theft.

The more plausible reason is that Apple and Microsoft have a cross-licensing agreement that covers these patents. So long as Microsoft doesn't make something that looks like an iPhone or iPad, they should be in the clear.

I think the most plausible reason is the same reason that Microsoft and IBM don't sue each other over patents.

Apple and MS have so many core patents that cover Windows, OS X, Windows Mobile and iOS, not to mention media players, office software etc. that any lawsuit will most probably end up in huge legal fees followed by a cross licensing deal after all the counter claims are decided on.