I believe bi-directional is definitely better, here is my logic;
Some companies make the claim that uni-directional winding is more efficient (I think JLC does this), some companies make the claim that bi-directional winding is better- in both cases there are massive financial ulterior motives for making either claim, true or not.
We know anecdotally, on a massive scale, that neither form of winding makes a significant difference to the overall population that wear the same watch most days of the week, even for half a day regularly. Things such as power reserve would be a bigger factor here. Therefore I believe that whether bi-directional winding or uni-directional winding is more efficient, is virtually a moot point, as the difference to the every-man is of such little significance. Further to that, the cost for servicing and service intervals don't appear to be significantly related to the type of auto-winding being uni-directional or bi-directional.
However, one point which is relatively objective, is that uni-directional winding is nearly always noisier, has rotor 'wobble' and spins freely in one direction that has a velocity somewhat felt on the wrist. Most people, but not all, don't like this sensation. It is more pleasant to have the least amount of noise, and rotor wobble on the wrist. In this regard, bi-directional winding is certainly better.
On a personal, somewhat subjective note, I also believe bi-directional winding must be better, because the angle in which the gears engage to change direction is so small and virtually negligible, when one considers that a minor flick of the wrist in either direction will likely spin the winding rotor many times. However, if the rotor is spinning in the 'wrong' direction on a uni-directional winding system, then it's not actually winding the mainspring, and further to that, all the kinetic energy of that movement is only distributed over the rotor and main shaft upon which it sits- rather than the entire winding works, mainspring and mainspring barrel.