While I don't necessarily think that history remembers Napoleon as evil, except in some very small circles, he did do many things that perhaps diminishes his reputation amongst his contemporaries and historians. To name a few for example: he abandoned his troops after the disastrous Egyptian campaign, he had himself crowned emperor (seen by many as megalomaniacal, at time when support for authoritarian rule was waning), he put his family members as kings of nations that he conquered (ie, Spain), and most importantly he was responsible for huge amounts of arguably unnecessary bloodshed in his wars of conquest, which essentially, amounted to nothing in the end (for example, almost a half million men perished in Russia, and that was just one single campaign in one single war).

 

That having been said, however, Napoleon is still seen as a hero in countries today like France and Poland, and large part of his unfavorable press, like you said, could be attributed to British propaganda at the time. While Napoleon was no doubt a brilliant general, and probably on the same level as Alexander, you have to understand that, there were probably many detractors of Alexander in his time, and in the centuries afterward (they just probably didn't survive to the present day). And another main difference was, Alexander brought Greek (or rather, Hellenic) civilization to the places he conquered, and states that were created in the aftermath of his conquests continued to be Greek-leaning in the centuries aftewards, which probably contributed to a more favorable opinion of him. I am sure you will find more detractors of Alexanders amongst his enemies, most notably, the Persians.