MGS2 is a mess indeed, but I can encapsulate much of it for you guys.
Snake and Otacon are now members of some group called Philanthropy, it's now their dayjob to go around and fuck up Metal Gears. A new model is being shipped, Snake gets sent in to take pics, Ocelot gets pics taken of him instead and slanders him on the Internet (no seriously) then sinks the tanker. The Big Shell is built to clean up the oil, then they sink a dummy tanker to pad out the cleanup while the Big Shell is just a big fat cover-up for Metal Gear RAY housed underneath.
Raiden gets sent in and we basically repeat the events of Shadow Moses with barely some innovations here and there. Whiny, bitchy, unlikeable pretty-boy created to troll fans who demanded more (because Kojima knows people wanna be badass but can't so he trolled everyone but everyone missed the point and raged).
By the end of MGS2, Otacon loses his step sister, the RAY's are mostly destroyed, Manhattan got a bad case of Arsenal Gear shoved into City Hall (censored due to 9/11) and Raiden has killed off Solidus Snake, who killed Raiden's parents so he could adopt him and make him the soldier he is. Everything turns out to be a giant replay of Shadow Moses, part of the "Selection For Societal Sanity" program (the S3, or Internet censorship). Somewhere between here and MGS4, Olga had delivered her child, Sunny, who is then adopted by Otacon by the time MGS4 rolls around. Dead Cell is finished off except for Vamp.
The more fans demanded, the more sick and tired Hideo Kojima got of the demands and trolled you harder with more fourth-wall-breaking until, when Konami got sent death threats if Kojima didn't direct MGS4, he torched the franchise and ran. Or TRIED to, anyway.
As for games I consider non-canon: Splinter Cell Double Agent and everything after. Each game kicked more ass then reached the peak with Chaos Theory, stumbled really badly with Double Agent, then plummeted straight down to the Earth's core and beyond with every sequel thereafter.