I liked Celerygirl’s first and last color schemes from her Wednesday post. I wouldn’t remove the shutters since they are totally architecturally appropriate to these windows and this type home. I would most likely also add them to the second floor windows since that is the way this style house would have traditionally looked. I like the bed line Yardvaark sketched out which looks great with the classic architecture and doesn’t hide it. I wouldn’t put anything much above window sill height across the front of the house.

While it will shrink your side yard, you might consider planting a couple of rows of cedar trees or other evergreen trees or shrubs )that keep their leaves year round) to create a "green fence" between the railroad track and your home. Not sure it would help with the sound but it certainly wouldn't hurt. After you plant the first row, plant the second row with those trees/shrubs blocking the view of any space between that first row.

I agree with Patricia Colwell and the others - remove the "Tudor" trim. I like the idea of painting the white stucco (after you repair it) to either the sage green or a color within your brick. pricklypearcactus is right about the sliding glass door entrance. Make that entrance a proper front door. Your home will be much more desirable when it comes to selling to have an actual front door (with sidelites since you have the room) rather than a sliding glass door entrance. Don't forget to put in a wide welcoming walkway and beef up your landscaping too like the insp pic below: If you go with the darker siding and change out the SGD, you could end up with a very attractive home (preferably without shutters!) like below.

"weird saggy edges like ours" ... I thought you actually had a sagging roof! Good grief, your house is lovely!! I would do nothing to it except hire a good landscaper to evaluate your landscape and carefully prune as needed. I am not a fan of gray houses, but it looks good. Very nice coach lights on each side of the garage (make sure they are large enough), and a lighter door color and some lighting under the porch roof, and you're good to go. On the right side, I would put a fence that comes out a couple of feet, and then across a couple of feet to hide the garbage can. Could even do something pretty with an arbor and some colorful plantings there. Nothing the matter with this house! Embrace it and the fact that you have awesome landscaping around it :)