Just found this quote from an interview with Kojima on why they changed the voice.
Kojima - "Regarding the change of voice with the new technologies we are now able to express emotions not only with his voice, but also with the expressiveness of the faces. The main theme this time is revenge, and so far the thrills of Snake could not match the words, but now that emotions can be expressed also with the faces we needed a real actor, not just a voice actor. For this reason we decided to use Mr. Sutherland."
Still think its the wrong decision and Hayters voice made the character who he is since MGS1 in 1998.