Fans were hoping for him to show up in the next game, though that didn't happen.
Achilles, due to his combination of humor and pessimism.
The fact that he has one of the funniest conversations in the whole game helps.
Benjamin Franklin, despite the small amount of appearances he has in-story.
Like Achilles below, he plays a major role in Assassin's Creed: Rogue, which takes place before III.
From Assassin's Creed III, there's Haytham Kenway, the Decoy Protagonist of the initial sequences, who's been compared to a seventeenth-century James Bond, and is some circles is considered more interesting than his son, the main character.
Revelations has Yusuf Tazim, the snarky head of the Istanbul Assassins, who still manages to kill several Janissaries during his Last Stand.
Deviantart has lots of fanarts showing him molesting Ezio or the poor, scared shitless Leonardo Da Vinci.
From Brotherhood, Cesare Borgia garnered this, mostly for being a male example of Evil Is Sexy it seems.
Subject 16 / Clay Kaczmarek, by dint of his Woobie nature and traumatic backstory, which eventually resulted in his getting a DLC pack for Revelations.
bombastic nature and abundance of character.
Bartolomeo Da Alviano, on account of his.
The quick-time option to hug him has led to players claiming to have restarted the game after missing it.
Leonardo Da Vinci, with his sheer Adorkable nature and enthusiasm.
pretty much all the supporting cast, basically. Claudia, Uncle Mario, La Volpe, Caterina Sforza, Machiavelli, Rosa.
Stinger, while not as popular, has his fans as well.
No player may consider themselves true AC fans if they don't know Nineball, owing to the fact that everyone has had their asses handed to them once by this guy and he won't hesitate to do it again. Unsurprisingly, (fan) depiction of her is with green hair. Practically no characterization, is an entirely optional wigman, and is never seen outside of her mech, but AC fandom in general and 4chan's /m/ in particular have fallen in love with the cheerful teenage girl in the bright green Engine of Destruction.
May Greenfield, from Armored Core For Answer.
In an official poll asking which couple was the most popular, Uzuki and the main character Kei ended up as number one. For the other party members, we've got Fyuria, Valeria (enough to be brought back to Agarest 2), Silvi, and Murmina.
In Agarest Senki for the protagonists of the five generations, Thoma himself is the most well-liked of the 5 protagonists followed by Leo.