(spoilers of TES series below!)
Lore-wise, I'm led to believe that the Champion of Cyrodiil is the strongest protagonist in TES series, seconded by Nerevarine, than Dovahkiin, The Eternal Champion, and The Agent in turn.
I like to ignore guild quests because it's simply implausible that one character becomes a guild master of every major guild in one province. I only took main quests of the vanilla game and its expansions into consideration.
The Agent was merely a competent agent.
The Eternal Champion was only a talented warrior who *barely* defeated Jager Than using the staff of magic.
Dovahkiin saved Tamriel, but Aldu'in is nowhere as powerful as enemies that Nerevarine and CoC defeated. (I've not finished expansions, so you could correct me if Dovahkiin has accomplished something greater)
Nerevaine killed 2 demi-gods and possibly killed another demi-god(Vivec has gone missing after Morrowind). The tribunal was powerful enough to defeat the avatar of Mehrunes Dagon who invaded morrowind and Dagoth Ur many times in red mountain, but Nerevarine had possibly become more powerful than all three combined, as the tribunal was no longer able to contain Dagoth Ur's power by Morrowind's time frame.
Nerevarine also defeated Hircine who sought to test him. I'm not sure if it was an avatar of Hircine or his real body, but even assuming its the former, it's still a remarkable feat to defeat a daedric prince in his realm.
The relative power of an avatar of Deadric prince compared to their real body is also debatable. I think there is not much difference, because Akatosh's avatar was able to defeat Dagon himself.
Then there is CoC. He didn't do much in TES IV's main quest, but in NoTN and Shivering Isles he defeated Umaril(deemed almost as powerful as a daedric prince according to some NPC) and defeated a Daedric prince in his realm, where one is nearly invincible. I don't think his position is disputable since he has become... you know, a daedric prince.
What do you guys think?