I think you can find positives and negatives in both commanders, like everyone in history who achieves some greatness. Genghis was the greatest of the horsepeople conquerors, following in the steps of the Huns and the Turks who had swept through much of europe and the middle east before.
Comparing the armies of Alexander and Genghis though, and which is better, is like comparing the Roman army to the Grand Armee. So much time had passed between the two's existence and the differences in technology.
