Board Thread:Questions and Answers/@comment-50.189.240.162-20140807193139/@comment-1672596-20140807194129

Kojima didn't exactly have any plans to continue the series, at least under his control, so I doubt it. Kojima even admitted that had he been serious about continuing the series instead of considering the current game to be the last, he would have spared Liquid Snake.

That being said, he probably had in mind Metal Gear Solid 2, at least, since the Meryl Lives ending did leave a lot of room for a sequel thanks to their dropping the hint that the President was not only an LET clone, but the one with ALL the genetics of Big Boss, a pure clone in other words.