It looks to me from the pictures that the rough spots are collecting dirt and maybe mildew. To see if it is mildew just put straight bleach on a dark spot and if it goes away then it is mildew. If that is what it is then you could just wash the house with a cleaner such as JOMAX and that will make your house look fine and if the paint is not peeling then that will be the thing to do at this time. If your house has not been washed since it was done then you are due for it anyway.
All those shingles are rough side out, (+/- a few). That`s sedimentry build-up, and mildew,...NOT MOLD. Mold rarely grows out in sunlight, ecspecially that much. Paint don`t do well on rough side out, if it were smooth side out, the water would run down the wall fast, rough side out allows the water to more or less trickle down and let the sediments collect. The mildew is from drying time.
Painted walls need routine maintanence periodically, it`s part of owning a home. Washing with chlorine products are safe on the paint/soil and keep the mildew levels down.
Less exposure and lace weaving on the corners, is water-tight. More exposure, trim and moisture barrier underlayment, is water shedding.