Video games with complicated storylines aren't inherently bad. On the contrary, some of the best games of all time feature totally convoluted plots, and gamer hipsters will tell you that an absolutely batsh*t narrative is the pinnacle of storytelling in the medium. However, nothing is immune to criticism, and all too often, enthused fans will confuse a complicated story with a good one. Just because a game features a huge plot twist that you never saw coming doesn't mean its story is finely crafted.
It's important to recognize when a beloved series has gone totally off the rails. While a studious player will probably be able to piece together what's happening in Silent Hill, the most die-hard fans are confused by parts of Kingdom Hearts, and sometimes, even a game's director will acknowledge that their story is just a bit too much.