Ideally, the thrust line should be close to the center of drag, so that no downthrust (or upthrust) is needed to prevent pitching up or down when the power is increased or decreased. Side area is very important in overall handling, since it damps yaw. Increasing the vertical tail area will make any airplane handle better when it is close to stall, but side area up front is also important, since the vertical tail needs area up front in order to develop the aerodynamic couple that is needed to resist yaw. If the fuselage has little side area, inertia steps in to supply the force couple, resulting in tail wagging, particularly noticeable if rudder is not handled just right at the exit of a stall turn. I did a lot of experimentation with adding a lot of side area up front, in the form of little vertical airfoils attached to the wings, and covered cabane struts on bipes. I found that it was possible to get virtually hands-off knife edge (no rudder input at all), but overall handling became a bit strange, with the airplane not tracking well in yaw. This is really just the equivalent of a tail-heaviness in pitch, transferred to the yaw axis.

I used to put the horizontal tail in line with the wing, but have run into a problems with two or three airplanes with such layouts. The symptom is an infrequent, uncommanded sudden pitch up or down when flying at a certain lift coefficient. I think that the problem is that the small burble that trails back from the wing may flip from one side to the other of the horizontal tail, resulting in a sudden small change of tail lift. I fixed the problem by increasing wing incidence by maybe half a degree; slightly decreasing the incidence would probably also be a fix. I now put the horizontal tail at least half an inch out of line with the wing, and the pitch problem has never recurred.