I'll suggest complementing nature rather than trying to blend in. Shingles same as the siding -- change in texture, not color. I don't see traditional-transitional here, rather an attempt to craftsmanize a house that lacks any resemblance to craftsman. I noticed you have not started an ideabook, so no way of knowing your style. Is your builder/designer/architect unable to do color renderings like I showed above?

The window trim change would be to Craftsman style. Unless you are doing the work yourself it seems a lot of expense for little difference on upstairs windows. It would, however, be extremely easy to do on your front door as you would only need to change the top board. And you could replace the side lights with solid wood inserts, or you could use textured glass that would obscure the view while still letting light in. While the limestone exterior is very light it has a yellow hue. Simply speaking the easiest way to find colors that work with the warm limestone is to choose a nearby color. That was probably why the trim is green. Since you prefer a modern look, I suggest you keep your siding light and use color only in the trim. Below are two combinations that I like. I darkened the roof color in these pictures.

I actually love the current color scheme because it's so classic. In my opinion, I think what you need is a portico since your front door is inset between the bay windows. A portico would modernize it because the current detail above the door is a bit dated. For the backyard, its a bit grey. I think you need larger trim around the windows. Then gel stain the pergola a darker brown to tie tot he brick and roof. Beautiful house!

Barnes, I am going with the Dove Wing on the entire house! My husband wanted gray with white trim but I convinced him that all Dove Wing would be beautiful and beachy with all the cable railing. I hope I am not mistaken! My POA is requiring a darker color on the stucco pillars/lattice. I'm thinking brown, gray or even a muted olive green to tie in with nature. Thoughts?