Gonna be a negative nancy and make my own thread to counter Wolf's.
Preferably this will be for games you actually likes. For example, Star Ocean: Till the End of Time had a troutty ending but it was a troutty game so that made sense.
I think one of the most infamous examples, and certainly the most recent one in my mind, is Chrono Cross. Frickin' love that game but everything kinda just fell apart after Chronopolis. I even liked parts of that tower at the end but then it was followed up with...well, you know.
Also for the purposes of this topic, let's just ignore Mass Effect 3. Please? It'll swamp the thread if I don't ban it.