I think that when you can do the same flooring in all areas, it will look better as it will make your space look larger and more cohesive. Also, if you have same species, you'll have ability to refinish the whole area later a different color and the stain color should be consistent.
While I love gray floors, gray is also more challenging to decorate with and also it doesn't always go so well with adjoining wood floors (unless there is a big contrast and cool tones such as dark - e.g. dark walnut, jacobean, ebony).
Re: transitions, that shouldn't be a problem. Just buy matching transitions made of the same wood. I'd be more worried about the colors working well together.
You may find these articles helpful:
http://theflooringgirl.com/blog/tips-on-matching-new-and-existing-hardwood-floors.htmlhttp://theflooringgirl.com/blog/5-ways- ... arger.htmlhttp://theflooringgirl.com/blog/red-oak ... rence.htmlDebbie Gartner
http://TheFlooringGirl.com