There are, roughly speaking, two types of generals: maneuvering generals and attrition generals.
However, I think Caesar puts them both to shame, demonstrating successfully both attrition and maneuvering strategies in his campaigns to great effect.
Tis a shame Caesar died so young (well when he was 55 anyways,) a brilliant politician and military strategist. I believe Alexander also portrayed both attributes, but his actions were more militaristic and his "political" success was most likely due to his acceptance of foreign culture and his willingness to give back a measure of authority to those he conquered.
Both were brilliant men though, displaying equal ruthless characteristics as well as consistently showing off respectful attitudes. Both diligent and both may have believed themselves demigods.
But that is off topic, as this thread has nothing to do with those two men...but Napoleon did have that aura that made him God-like, making him a cut above the rest. This is what defines normal men from others, making me believe that Napoleon was the better general, even if it lead to his demise.
The Spanish soldiers were renowned for being useless. The partisans were arguably the greater threat. They proved that in the peninsular war and countless other wars before and after.
Wellington was a defensive general. He had to command a much smaller force than those of Napoleon, and he had to fight a huge potential French ground force on the peninsular on top of limitations on cash grants from a unfconvinced Government and lack of reinforcement promises. He specialised in choosing his battle ground perfectly, holding a defensive position and relying on the better training of the British forces to prevail. He also knew when to retreat in the face of overwhelming odds in order to better position himself to eventually rebalance the game. Wellington also knew how to properly supply and move an army. It may not have been with speed, but rarely were there cases where his men were without supplies, as happened with Napoleon. He also came up with the remarkable military system that allowed British armies to adequately move heavy equipment throughout the interior of India.
Napoleon on the other hand was far more tactically agressive. His speciality was in commanding armies of great size, or several armies of smaller sizes, at great speed in order to catch his opponent off guard. He'd then exploit this and force columns through the weaker spots in an enemies army in order to split them. His system of promotion upon ability and division of the spoils of war were also remarkably modern in their time. Something the British would be slow to replicate many many years later. However, this also led to his need for living off the land, something that was his downfall in future events. He also bled France dry. By the time Waterloo came about most Vets from pervious campaigns had been killed and the troops were Fresh young faces press ganged into his armies in order to meet his demands.
All in all, you can't say which is better. They both had their strengths and weaknesses. Napoleon's early career demonstrated remarkable Generalship and was probably the better military leader until his status as Emperor and ruler of main land Europe got to his head. He chose to fight on too many fronts. Wellington on the other hand knew he could not tackle his opponant head on. His task was to lock down as many resources as possible in the peninsular, and to prove that Napoleons armies were not as invincible as they were perceived. If by definition, we take Generalship to mean the ability to recognise positions of strength and the ability to get the job done, then they are probably equal in terms.
We also have to consider culture. Napoleon was a true flamboyant, passionate, extreme Frenchman. He had the ability to inspire his soldiers to great feats. Wellington was the typical, solid, take it on the chin style Englishman that would later be so stereotyped (based on Wellington's personality). He also had the ability to inspire those soldiers around him. So if we take Generalship to mean ability to inspire, then again I think they are also relatively equal.
As to the Nelson, Wellington argument. It is unrelated. Yes in the modern era Nelson is probably the more famous, however, in those days both were seen as heroes. Nelson's carriage was unhorsed and carried through the streets following his return after the victory at the Nile. He was a well known name and a considered to be the one true hope against the threat of the French 'tyrant'. However, the Battle of Trafalgar is actually over played. Whilst it was in no doubt a remarkable victory, Napoleon had already given up all plans to invade Britain following a storm that destroyed his invasion fleet, and the French Meditteranean fleet had already been all but destroyed at the Nile. The Atlantic fleet that fought in joint with the Spanish fleet at Trafalgar was all that was left of the French naval force. It was simply the final nail in the coffin.
Wellington at this point was still relatively unknown, don't forget he was infact younger than Nelson. But following his later victories and Waterloo itself, his carriage was also subjected to the same treatment (albeit in true Wellington style he abandoned it long before he got there due to his constant hate of any form of hero worship) and was a seen as a great military hero himself.
In reality Wellington and Nelson were just as important as each other. They were completely opposite personalities, Nelson being the reckless, charming typical hero and Wellington being the calm, cold aloof gentleman. But they both commanded a similar level of respect following their victories.
These were the only two educated and accurate posts in the thread. Both were specialized generals who had the opportunity too show off their brilliance, something which is rare today.
Too tell you the truth I believe there were more brilliant man that have walked the earth, two of them mentioned earlier in my post. Even so, they were a cut above the rest, better than most at what they did...but how many times have many generals been given that opportunity? Since Napoleon seized that opportunity for himself I am more inclined too lean towards him, while Wellington was a response to him.
Napoleon defiantly strikes himself as a more interesting character, in my opinion of course.