I finished the game last night and didn't even realize I finished the game until just now. Spent 6 hours running around mother base and doing side ops hoping to trigger Chapter 3 somehow. I really liked the plot twist but are they really going to end the game there? Are they really going to let the whole "bunch of kids stole a giant mech and a biological weapon" thing just hang there and not resolve it? Am I really supposed to watch a youtube video with unfinished cutscenes to get closure on this 100 hour epic I just poured my life into? It is so weird that a game with this much content, quality and attention to detail is left without a proper ending.
You have to remember, Kojima was fired during development. Odds are he had a certain timeframe he had to deliver the game before he was out the door. Under different circumstances I bet it would have been delayed at least until the end of the year.