While in theory All MGS games are exactly the same fundamentals, there are some relatively major differences in 3 as opposed to the other two.
No Radar, this would mean that you cannot rely on looking at your radar but by constantly looking ahead of you and planning your moves.
Alerts can last up to five minuites, skulking around in hiding is horrendously tense when an alert is on.
You can shoot helicopters and other vehicles etc.
Much, Much Longer. I have been playing for ten hours and have really only got 50% through (I assume). The other two were possible to complete in 6 hours if you knew what you were doing.
Finally, MGS3 is relatively hard (in comparison to the other two), but once you play for a long time you get used to it and it becomes natrual to sneak about.