IMO those windows do not suit this house. I am glad you are removing those silly shutters. What are the larger windows going to be like? I can’t see that there is much space at the top of those windows for larger trim on the main floor but you could add some to the upper windows.

Aside from removing the shutters, which accentuate the asymmetry although I'm sure they were meant to ameliorate it, I think you could do this -- straight lines over both side windows makes it less obvious that they don't match. They look more as though they were placed in proportion to the width of the wing. Aside from that I advise you to get some really nice landscaping in there, to draw the eye down. I think you might also get an architect to redesign your front steps, which seem too narrow to me. Paint the garage door to blend with the brick, or to match the roof. It really is, basically, a lovely, dignified house. But the architect responsible should be shot for messing up with the window placing/sizing (the right window should be wider). Grrrr.

You have plenty of room for arched, correctly-sized shutters. It's an option, not a necessity. If you do add shutters, also add them to the garage. Speak with a local cabinet maker, or try to find a local woodworkers group, custom-sized shutters are pricey.

The trim is weird, though I did just have wider trim put on the rest of the windows and corner boards, but the original trim was not bad, just a little narrower than I wanted. The carriage doors unfortunately will be replaced soon with overhead doors as they let in too much cold air and there is finished living area above the garage. The new doors will be trimmed with the same arch to retain the look. We also have plans to add an overhang, as well as a third bay.