I played MGS2 yesterday and your point is kind of true. Also MGS2 was the first MGS I played, hence it's my favorite.
The point is it is MGS1 again, that's part of the plot and thats cool. But that doesn't change the fact that the game doesn't play it safe and at time's refuses to give the player what it wants. MGS fanserivce isn't the problem, no they all have that and that's part of the series charms.
MGS4 on the other hand is not simple "hehe references and being meta". It's problem is that it tries to answer everything with the sole purpose of appeasing fans. Previous MGS games weren't exactly interested in that. People have powers, eh whatever. Strange stuff does not need a logical answer. But 4's main story reason to exist as said by Kojima was to answer all those questions people wanted answer.