On one side of the roof I replaced every rafter due to rot and woodworm whereas on the second side I just extended each one down so it will cover the future external insulation as these were all sound. Where the rafters were replaced everyone had to be cut to a different length due to the building being out of square, this made it a bit of a slower job, but its only a small roof!
I decided that although the specifications said to insulate between the rafters and on top I made it a "warm roof" and insulated only on top, this keeps the air flow between the rafters but used a more expensive insulation to meet regulations - the building inspector was happy with this solution.