The elevation diagram is not the best thing to use when trying to figure out your colour scheme. It doesn't give a very realistic idea of what things will look like at all. If you're going to try re-colouring a picture, the best option would be a picture of an actual house built from this plan. Second best would be a 3D rendering of the house. You can use any graphics editor to do re-colouring. I like gimp. It's free and does pretty much everything Photoshop can. But if you're not up for learning a new program, coloured pencils and printouts are a good way to go. If you're working with an architect, they should be able to produce 3D renderings in a variety of colour schemes-- and that would be the best option by far.

I would stick with all lap siding. The house has a nice horizontal feel to it and adding board and batten will fight with the horizontal feel of the house. And adding shakes will cut the house making it feel more squat. It's a cute house. Don't try and make it something it isn't. I'd play up the porch and entryway and tone down the garage by making the garage door the same color as you choose for the house. Definitely go with Hardie.

What I see ... a tract builder interpretation of a modern prairie style home or a basic hip roofed colonial circa 2000 with "modern" windows. What style were you going for? Did you use an architect? What does "modern feel" mean to you?

so much depends on how you need to use the space(s) you look set back, I would enclose or create a private seating the Aqua door area with the verticle windows into a patio with a pergola over top... Landscaping will add a lot to the front, a porch, not so much. a bigger landing, yes. I don't like the bow window, but I don't know how you will use it from the inside. I'd make it a flush window and make a walking path from the other aqua door to the front door.