When Keifer was allowed to register a blip on the emotion monitor he was pretty good, but Hayter put his all into it constantly. He eventually made Solid Snake, Big Boss, and Old Snake all sound different in subtle ways, and I really feel he strained his vocal cords for the latter two in Peace Walker and MGS4.
I don't exactly mind Keifer though, I actually think it would have been pretty cool if Hayter handled Ground Zeroes and Keifer did TPP, both trying to mimic each other's voice so it's a natural progression. It makes sense to think that Snake's vocal cords got messed up after a 9 year coma, so I don't think it'd give too much away in regards to the final twist. Hell, it makes less sense the way it is now (did they massage Venom's throat to make his vocal cords match EXACTLY?)