Title says it all.

To me, Kingdom hearts and Metal Gear solid series are among the worst exemple I have in mind. Damn, when you think of it, the first MGS and the first KH were fine storywise. They was no need to complicate things like they are now.  

Nothing beats Kingdom Hearts.

Seriously, Metal Gear is tame compared to how convoluted Xenahort's story is.

Replaying Resident Evil Revelations right now and it's pretty darn bad. Everyone's a good guy and a bad guy, there are a million different organizations and groups, and everything is an elaborate setup. Remember fighting a crazy dude in a castle because he's a crazy bad guy? I miss that.

*looks at Sonic 06*

Don't worry, I'm looking at it too.

I join both of you.

I remember spending a whole night discussing the plot of Siren: Blood Curse with some friends.

Bioshock Infinite is pretty deep.

I thinking about making a thread like this once to find more interesting stories to play through.

Kingdom Hearts.  Its story isn't even that hard to understand but it just went across so many games.

Try Resonance of Fate.