I love yellow with a green roof:

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I like Tres McKinney's suggestion for main body in taupe/gray or gray/green and the trim slightly darker. But I would also consider adding a pop of color as Lindsey suggested w/a cayenne red front door to increase the fun and welcoming factor of a cottage home.

Tres, I think your suggestion is where I was heading with my second pic; I'm just not a huge fan of taupe/greige personally so would rather see the wood tone of the shakes continued onto the siding.

But taupe would look very good, of course.

OP, if you are planning to change the roof in a couple of years, maybe it would be best to choose the colors you love regardless of the roof color, and consider your future roof choice in your decision. You might have to live with a clashing roof for a couple of summers.

Is this visible from a lake or river? I always think the cottages that are the most compelling are the ones that include a natural but obvious color: olive green, maroon, burgundy, mustard, navy, cayenne...all these colors blend into the landscape, but still draw the eye in to set the imagination whirring :) And add interest during the more bare and brown winter months.

You need better landscaping more than color changes.