Alien Isolation

The game doesn't have to be super long to be bloated with fluff.

My pick is Bravely Default. The entire 2nd half of the game shouldn't exist and it would have been a much, much better game. I also believe that Project X Zone overstayed its welcome. Single SRPG map shouldn't take 90 minutes to beat.

Alien isolation. I loved the game but it started to drag at the end. 

Also, unusual answer: Rome Total War. Great game that helped Total War reach the high, high peaks of Medieval 2 Total War and Shogun 2 Total War. However, because of the way recruitment worked and the sheer size of the requirements for victory, for most nations the late game becomes an incredible drag. Add to that that usually by the end when you are a massive super power there's another major, major power under NPC control that will probably both declare war on you and hold territories you need and you have a recipe for an absolute slog. Do you have any idea how much of a drag it is to try and mobilize the full military might of half Europe in that game?

"Even though you just saved my ass a few days ago, I STILL don't think you're worthy of being labeled as the chosen hero, so despite the fact we're in a race against the bad guys to save the goddess, I'm going to waste your time and make you do the most pointless shit that won't help you at all in your quest because I'm bored as hell and I have absolutely nothing better to do!"

-MF'ing Water Dragon

Darksiders 2. Great, but the "there's 3 of everything"design was repeated too much and got old
God of war 3. Yes it's already a bit short..but everything after beating Chronos sucks. So it should have ended there.

There are many more but these are the ones I remember right now

every Keoi Tecmo game