You need to make a serious effort at setting up a list of considerations. I would most definitely separate into a minimum of two catagories: Strategic command and Tactical Command.
Strategical, one should look at the overall scope of what the general accomplished. Alexander and Temujin together conquered the greatest territory in pure mileage yet both were sole rulers and thus had great advantages in how they shaped their empire and one tends to think of them as the best strategic commanders, but were they? I would posit that because they were supreme rulers that this actually diminishes there accomplishment as generals. The reason for this is simple, the added element of ruler and commander is intrinsically important skill of a general. One needs only look at Belisarius or Hannibal to see what can happen when Ruler and Commander are not in sync. Does this qualify Belisarius or Hannibal as better generals than Alexander and Temujin strategically though? No, it's merely one category of many we need to define before we can quantifiable engage this question. Hannibal lacked siege weapons and the ability to bring dynamis to his troops, albeit much more difficult because of their mercenary nature. Belisarius never lost a battle but did lose his emperor's support through lack of political acumen on his part (and his inability to remove insubordinate underlings, namely Procopius) Caesar shows tremendous potential here in both his ability to manipulate his ruler (via the triumvirate), his troops (who would fight in his name years after his death) and his overall campaigns; however, his inability to thoroughly crush his enemies as his successors did (Antony and Octavian) through proscriptions should be considered, assassination is defeat - plain and simple.
So now we have several sub-categories within Strategic command:
Relationship between general and ruler (or rulers as the case may be)
Relationship between general and troops
Total Territory conquered
Sustained empire (both during lifetime and subsequent century -- it is foolish to suspect even the greatest general can forge an empire for 5 generations without a great deal of luck)
Clear Winner: None
Tactical command is entirely different. Here we are concerned with only short campaigns, skirmishes and pitched battles. Remember, adversity reveals the genius of a general. So 100 victories against peasants means nothing. Alexander for example faced an army that was simply unmatched by his troops and more importantly diminished by Darius's multiple flights. Still, one should consider his singing skills, which were unparalleled save by Demetrius.
Temujin early campaigns were oft ill prepared and he suffered several major defeats which tamper his consideration for best tactical commander. Hannibal's defeats at zama and the naval defeat at Eurymedon river tarnish his otherwise phenomenal career. Caesar's defeats in Egypt and at Gergovia are equally important though he rebounded and defeated the same commanders utterly in both cases. Belisarius perhaps remains the only undefeated general then but one should consider that his fights against the Ostrogoths, Vandals and Bulgars were ones where he had better troops though was often numerically inferior.
Sub-categories of Tactical command:
Troop quality
Numerical advantage or disadvantage
Were losses overcomed?
Siege skill?
Clear winner: None
Conclusion: We need to identify and expand the qualifications of a general and how we wish to quantify his skills before any convincing argument can ever be made.