I too thought that nonomacines got a lot of love from MGS4. I mean in the first 2, you knew they were there, but it wasn't a really big deal. I think almost every plot twist in MGS4 had something to with SOP/nanomacines, but I thought it was good anyway. I'm definitely gonna miss the series.
I don't really have a definitive answer as to how Ocelot has so large a military, but if I had to guess, I'd bet he always had it up his sleeve. You remember all those phone calls at the end of the other games? This dude has some serious connections! Maybe I missed the explanation in the game. If so, enlighten me.