I think you might be responding to the discrepancy between the overall form of the main house and the craftsman elements superimposed on it.

Essentially the house, including the elongated upper windows, and the strict symmetry of the underlying form is a Neo-Classical house.

If you want to do a craftsman style you have to reduce the verticality of the house. The symmetry is dictated by the floorplan, but I would try to make it look more asymmetrical as well. You actually need Less rooflines to do craftsman with a heavier more imposing "brow" on the house which would mean getting rid of the peaked roof over the two upper windows and creating a shed doormer over the center, if not just eliminating it altogether.

The windows in the small dependency between the garage and the house look really dwarfed by the amount of wall around them. They should probably be bigger. You might also consider a hipped roof on that area as well.

What purpose do the two story bay on the right and the oriel on the left serve on the floorplan? You may want to further break the symmetry by eliminating that element on the left altogether.

Could you turn the garage sideways?

Also I think that the post and beam porch really comes out of nowhere, and you may be attached to it because it represents the original idea.

I know this sounds like a lot of objections, but I think that you understand that the house just doesn't "look right" or you wouldn't be questioning its appearance :)

Here are two Pasadena Craftsman houses that are large and fairly symmetrical to illustrate the difference. These have a broken symmetry, or are more balanced than symmetrical, These have full or wraparound porches, but that is not necessary to the form--it does help emphasize the horizontal, though.

This isn't a complete thought but this is closer to craftsman than what you have developed:
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Hi Karen,
Its funny because I am in the procces o begining a house that is very simlar to yours. I am posting my front elevation.

There are a few things we did to help break up the look of the front and give it that timber frame classic look.

The walkway between the garage and house is a mudrom area so we gace it a door with a small awning over it to match the main porch.
You center box roof also might look better if you pull it forward and make it the strongest point of the house. That is if you like the symmetrical look.

As for the craftsman look, just by choosing the right windows you can help that.

Thanks palimpsest! I am not sure if we can make such big changes at this point but it both comforting and unsettling to know that my intuition was correct. I'm wondering if getting rid of the timber frame porch, making the right towerish piece wider (we cannot get rid of the left bump out element, it holds the bath tub) and extending a more craftsman like porch to the left would help. I have to see what we can actually change at this point. it has already been appraised by the bank and I do not want to have to go through all of that again. we will be breaking ground in September. The picture shows more of what we were looking for after we dropped the mountain house plans. I wish we had brought up our concerns sooner.

BradinMass, wow that is very similar (but you plan looks beautiful and not pieced together) It is nice to see that if we cannot make too many changes then maybe a few will make it better.

It doesn't look like a Mountain or a Craftsman house to me. Is there a designer involved? If the design is borrowed from multiple sources you should get a professional designer involved ASAP. Don't let the trouble of getting another appraisal prevent you from protecting this large investment.