I found the plot of a given MGS game straight forward after playing it, including watching all of the cutscenes and listening to the codec calls. There might be some lingering questions to answer, but they're not really that important to the plot for that game.
The problem is later games build up on previous ones. Including said points that weren't important for that game. i.e., that whole thing with Liquid's arm on Ocelot was a minor point in MGS2 but a major one in MGS4.