Designing a timber framed home requires the simultaneous development of the floor plans and the timber frame. In order to capture the essence of the frame it needs to work well with the flow of the plan. This is achieved more easily when walls line up with heavy timbers at the juncture of individual bays, or as another example when outer wall posts outline the space and allow for the natural placement of windows and doors. And its not that this feels contrived, it can, but the best plans are those where it just "feels right". There should be a flow and coordination between the framing and the functions within it, it should work so well that you don't notice it. The affect is natural, organic, in that you're not sure which came first, the frame or the plan.
And actually that is entirely true, because the only way to achieve this is to develop them together. While some might see timber framing as very constrictive and limiting in their choices others see it as liberating. Since the timbers take care of the structure of the house you're free to use the space within freely, your partitions and rooms can go pretty much anywhere since, unlike conventional construction, the walls are not bearing walls playing a critical role in the structure of the house and limited in where they can be located.
I think that sometimes when people feel constricted by their design options in a timber framed structure its because they would like to "paint" a floor plan onto a blank slate without any consideration for structure. "Form follows function" is natural, we are creatures of this planet, familiar with shelter and structure. Why wouldn't we design that way, isn't it logical that we are most comfortable within that which we are most familiar? A timber frame is built from natural materials that by their nature must respect the laws of nature (physics) or face an early demise. It is "harder" to design when faced with limitations (such as gravity or financial limitations), but if it was easy why would you need a professional? It is not hard to design a house, but it takes experience and hard work to do it well, and is especially challenging to do it well and to have it meet your budget! The scary part is that if it isn't done well enough to meet your budget you don't find out until its too late!
I find that plans come together if you work at them hard, keep an open mind, and let them grow naturally. It's not unusual at all in the design process to have to take a "time out", and just let it mellow for a while. Its not like you're just watering it and placing it in a greenhouse, but somehow when you come back a few days or weeks later its grown on you, you see things differently and suddenly a new idea strikes you, a change here resolves an unrelated issue there and voila! All of a sudden the pieces start falling into place and it seems to lay itself out on its own volition. When this happens its very exciting and its one of many reasons I love this work! To be able to share that excitment and those "eureka" moments with a customer and enjoy their passion vicariously for their new home, is something that gives me the energy to keep pressing forward on a difficult design problem, because invariably there is a solution.
Ludwig Mies van der Rohe said "God is in the details" in reference to beautiful architecture, and architectural design. Design is one of those activities where it does pay to "sweat the small stuff" and get it right!