MGS4 assistant producer Ryan Payton's spilled a pretty big can of beans in this 1UP interview, saying that the MGS trilogy on PS2 was never meant to be continued.
"The stories of MGS2 and MGS3 were truly written without any backup measures if the series continued, leaving dozens of confusing and unexplained plot elements in the wake," he told the site.
"The fact that we were able to tie up all the loose ends with MGS4 was nothing short of a miracle."
Payton left Kojima Productions after the launch of MGS4, citing family reasons.
Heaps more through there. Even on a cursory glance, it appears to contain a huge amount of spoilers, so be warned.