This is complete conjecture on my part and could well be completely wrong.
His connection with Microsoft may not be completely severed. It's in Microsoft's interest to ensure that there is continuing doubt over whether or not Android is patent-free so they can continue their shakedown of handset manufacturers, so having some "expert" out there sowing the seeds of doubt every time some little claim of infringement appears would obviously be beneficial to them.
As far as I can tell, his predictions on Oracle vs Google have been pretty accurate, despite being at odds with other commentators. Shouldn't we be looking at how predictions match reality, rather than how they match other predictions?
The only dispute I can recall about damages was many people claiming that Oracle had lowered its damages claims, and Mueller saying they hadn't. When the full damages report was released, it turned out Mueller was right - they changed methodology, but the overall figure did not go down.
It's true that the judge has been hard on Oracle's damages report, but I don't recall Mueller ever saying otherwise. He's always said that they key issue is Oracle's ability to get a permanent injunction rather than money damages for past infringement.
He has some strange axes to grind. I just can't work out why (or exactly what his precise angle is)