The main reasons for this refusal is that they are alterations to a listed building, which although would normally be considered perfectly acceptable to a house, are considered inappropriate to the listed building.
The drawings and the scheme are quite clean and simple but with listed buildings, the listing is in place to protect the original fabric and character, thus the proposals are seen as too extensive.
PAPA Says - Meet with the conservation officer, establish the key issues and revise the scheme accordingly, if you cannot overcome their issues consider consutling with a qualified heritage consultant.