Crystal Dynamics' take on Tomb Raider could be considered a controversial one...
On one hand Eidos did start it all and the originals were great, I mean you can't condemn the ps1 graphics, the games themselves were good, even if it was the first game 5 times in a row technically

But I really love Angel of Darkness, the story and characters anyway. It's a shame that it was Eidos' downfall.
On the other hand, Crystal Dynamics have done a great job at bringing the series up to date, it might have taken a couple of tries but Underworld is a firm favourite of mine.
Then again, to agree with the OP, I should point out Climax and Double Helix, of Silent Hill Origins/Silent Hill Shattered Memories and Silent Hill Homecoming respectively. It never has been the same since Team Silent. Still, at least Climax are actually TRYING. Curse you Double Helix!