I've only briefly played Morrowind so it really comes down to the Eternal Champion or the Last Dragonborn. Judging solely based on the main quest and the direct qualities of the hero I have to go with the Eternal Champion. The Dragonborn has the ability to shout, giving him/her a pretty significant advantage over 90% of enemies. The Eternal Champion was just a person stuck in a jail cell who then escaped and decided to save the world not because they HAD to, but because they WANTED to.
This might also have to do with the Eternal Champion charging head-first into Oblivion as one of their first quests. Kvatch and Bleak Falls Barrow can both be regarded as the "starter dungeon", and while the barrow is pretty cool nothing beats running LITERALLY INTO HELL and killing demons/daedra with no backup and no idea whether you'll ever make it out alive again.
I always prefer heroes that grasp power than ones that just inherently have it. Sometimes it's nice for your protagonist to be 'special' but it's equally fun to have one that's really just some guy/girl who's just your average person who has to fight for glory every step of the way.
I know this thread is quite old now but I only just found this one anyway my favorite is definitely the Champion of Cyrodil since the Nerevarine is if i remember supposedly meant to be Nerevar reincarnate and the Dragonborn has the soul of a dragon whereas the CoC was just a normal person that achieved greatness rather than being born with it, plus he became the Divine Crusader and Sheogorath (although he was only Sheogorath in name only during the events of the game).
Saying that though I've only played the games from Morrowind onwards so I havnt experianced the heroes prior to Morrowind, finally sorry for any spelling mistakes or anything like that its 1am where I am so I'm kinda tired
I don't like the Dragonborn mostly because of all the advertisement there was about it. The whole cliché they generated about the Dragonborn having to be a bearded Nord male who wears the most useless helmet in game with a set of clothes that wouldn't even work with the perks (LA + HA) just makes me want to vomit after a while.
Even the community goes with it. Everytime I see someone trying to make artwork of the "Dovahkiin" or that makes a video where he's in, it's necessarily that one guy nobody ever even played in game. Like, seriously, don't people ever get tired of it?
Now my favorite... uh... Hero of Kvatch. Becomes Sheo. Good enough.