I know it's been mentioned several times but Skyrim. I actually took the time to platinum it, and in doing so realised that the whole experience had been designed around you being able to do everything in one playthrough, pretty much destroying any feel of true immersion.
I had completed half of the Thieves Guild missions when I joined the Dark Brotherhood, yet when I visited the guild for the DB missions nobody had any idea who I was, leading to one very odd conversation wherein a thief treated me as a stranger in one dialogue tree and then two seconds later congratulated me on finishing the TG mission I'd taken from him a few hours previously.
In short: by trying to let you do everything at once you never really built up an allegiance to any one particular faction, which resulted in an experience that wasn't bad but just bland across the board.
I had completed half of the Thieves Guild missions when I joined the Dark Brotherhood, yet when I visited the guild for the DB missions nobody had any idea who I was, leading to one very odd conversation wherein a thief treated me as a stranger in one dialogue tree and then two seconds later congratulated me on finishing the TG mission I'd taken from him a few hours previously.
In short: by trying to let you do everything at once you never really built up an allegiance to any one particular faction, which resulted in an experience that wasn't bad but just bland across the board.