My favourite so far is 3 - great boss fights (especially The End) - lack of traditional MGS radar (enhancing the sneaking element) - great story that puts an interesting twist on the previously established story of Big Boss.
I'm glad (/I hope) that the MGS series is done with 4. But with Solid Snake's story done, if they want to make a new series in the same world, the thing I think they'll need to do is come up with a protagonist with an interesting story. That was ultimately what drew me to the MGS series in the first place. I think it could be done with Raiden, given the story we've already been given in 2 and 4. I agree that Ocelot is a very interesting character but I don't know how he'd fit into the role of protagonist. He was always more of a schemer whereas the heroes in MGS games tend to be the victims of schemes.