It's funny, as I think Alpha Protocol is much more favored than not - except by the mainstream media. It's one of those games that actually deserved the media bashing, but let's not get into that
I probably have dozens of examples, but the one that immediately leaps to mind is Hellgate London. It was heavily flawed upon release - and the PR handling was very, very unfortunate. But the actual core of the game was fantastic - and I still think it represents the most visceral and satisfying combat of ANY action RPG.
Near the end of its life under Flagship, the game became quite stable and was well on the way to becoming the best ARPG of all time. Well, I think so.
But the initial release and the PR debacle had destroyed all hope of saving it.
Also, I happen to think the general response to the subscription option was short-sighted and stupid. Not at all unlike the way people expect all MMOs to be F2P today, and expect the games not to be negatively affected by it.
Oh, the wonder of the ignorant mainstream audience.