There are good reasons structurally for having such timbers directly opposing. If you remember back to any physics classes you may have had, there was a law "for every action, there is a reaction". By putting such members directly opposing each other, you are better managing the forces that may be put upon your timbers (wind, snow, roof weight, etc). An easy way to imagine what is going on is to think of the ridge beam....if there are loads from both rafters transmitting to the ridge beam, the loads are attempting to "crush" the ridge beam...this is ok in that the beam will stay "straight" because the forces are directly across from each other. With alternating rafters, you would have forces at various points attemting to move the beam....if you were to apply enough force at each point to cause deflection, you would in effect have a serpentine shaped beam...in addition, any joints involved in this activity have a "moment" or torque applied to them that may be eliminated if you have opposing beams or rafters. I have an engineering degree and these are basic "statics" principles but I certainly do not profess to be a structural engineer. This is a tough subject at best as forces can do some strange things and even engineers using FEA (Finite Element Analysis)have trouble predicting what can happen in certain instances.....again, like the other responses, things usually end up a certain way because of experience of what works and what doesn't...take the advice of what has worked in the past. A good rule of thumb...keep things simple and symmetrical or else call a structural engineer. Good luck and may all your projects be successful (or at least repairable!). Roger