You need to chose the refinisher then let them choose the wood they like working with. Pine is hard to beat for matching existing wood on remodels.

I think I have the same siding as you - it looks like Hardi Board. Those nail holes look wrong to me. If those are on every piece of siding then the original installer didn't know what they were doing. Except in special situations, the nails should be covered by the piece of siding above. There should not be nails down low on the siding. Since those holes should not be there, I would think that filling them would be an extra step. FWIW my neighbor has the same siding and the installer caulked the seams between the boards - the vertical seams. It looks horrible because the caulk is a different texture than the siding so it sticks out. Caulking those holes would probably give you the same result - strange shiny dots on your siding. Having said that, giving water a path into the siding is not good either. But if the house is several years old and that has not been a problem, you are probably fine. On the soffit - I would have someone finish that area with an appropriate soffit material that will accept paint well and hide the 2x4s and plywood that are there now. No amount of paint is going to make that look good.

If you like the look of the exposed window header, I would plan on 1x4 all the way around the window. It will allow the stucco to be cut back and for a nailing flange (and properly flashing) during the window installation. I like the architectural bronze or black color on the Tudor/Stucco combo, but this is all personal. Make sure they use a composite/PVC trim for long term durability. The rest of the questions are mostly color (i.e. personal), but I would go with a primary for the walls and one for the trim and that be it.

Thank you so much for your replies, Susan, Cat_ky and Litterbug. Seems like no one is in favor of shutters. Litterbug, yes, I noticed that the shutters on the front windows were too narrow to cover the windows. However, if we made them the correct size, I think they would look too wide for the wall space. The existing shutters on the garage windows are too wide to cover the windows so I guess shutters would need to be two different widths. I was worried that eliminating the shutters on the garage windows would make them appear too narrow but I think I'm leaning toward framing all of the windows in 2x6 to match the side windows as Susan suggested.