The second grave is forJust got there. I thought the ending was kind of cute as well... sort of like the start of Act 4. It all ends up being one long interactive cutscene though, still, it was kind of neat.
At the end, one grave is for Big Boss... but who is the second grave for?
The Boss, Big Boss's friend and mentor whom he was sent to kill in MGS3. All the trouble in the MGS world is because people are trying to carry out her ideals, but are failing to do so
The whole thing about snake saluting in the very beginning of MGS4 is an homage to a very emotional scene involving the above character in MGS3