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Splinter Cell is based on real-life black-ops. MGS is a similar style, but is more based on Japanese Manga - hence the giant robots the game takes its name from.
Other than the fact that they both have a stealth aspect, they're really quite different games.
In some parts splintercell is more realistic, for instance life but unrealistic for instance talking by sam fisher when your just about to grab a guard but the story line is really really bad.
But in mgs3 you actually get wounds and have to eat but it does have electric guys, and guys who go invisible, but thats to make it more interesting and challenging. It also has a greater array of weapons. Splintercell is extreme stealth for those who like just stealth. But mgs3 is for people who both enjoy action and stealth and has a better story line.
Because of this i believe that mgs is better as being more inventive, realsitic and having a far better story line.