A friend and I have recently played through a handful of games together, switching off at regular intervals. So far the games we've played (Uncharted 2-3, Shadow of the Colossus, Dead Space 2) are broken up into chapters/sections of more or less equal length. I finally wore him down and convinced him we should play the Metal Gear Solid series (which took some doing; he's always been of the mind that MGS is just anime nonsense, while I'm of the mind that anime nonsense isn't necessarily a bad thing, especially as buck wild as MGS gets). Any advice on how to break up the games for our controller hand-offs? I thought about just setting a timer, but there must be a better way, right? Any ideas?

Switch every cutscene. EDIT: Switching every boss would work for every game in the series not just MGS1 as @shindig says.

Peace Walker is co-op but not local if you end up going that far.

I'd switch every boss fight for MGS1. The game usually has a couple of areas before moving you from boss to boss.

You could switch each time you enter a new area or die a few times.