Substance has a longer shelf life. SOL is pretty much over after you beat the game, Substance has all the extras to keep you busy, including more unlockables. The good thing about SOL is that the FMVs are less censored when it comes to blood and gore.
Chowser: Target has 4 PS2 titles on sale for $39.77 this week - MK: Deception, Spyro: A Hero's Tail, Tony Hawk Underground 2, and SW: Battlefront. The sale is good until this Saturday. Go to your local Target on Friday or Saturday and see which of these 4 games are out of stock, then get a raincheck and substitute MGS3 for it. Get 20% off instantly.