Given the overall anti-authoritarian thrust of the game, I think the Tracer Tong ending is the one that most fits with the overall theme of the game. When I chose that ending, it fit perfectly with JC's character arc and the story as a whole.
The other endings . . . not so much. The Illuminati ending was basically just restoring the old order to what it was before MJ12 split off. What is to stop a group like MJ12 from splitting off again? More importantly, MJ12 splitting off was a function of the power and lack of accountability that the Illuminati had. Helios is the same, just write large. Granted, I chose the Helios ending because that makes the most sense to me personally (TT's just hits the rest but does nothing to prevent the same situation from arising in the future while killing a lot of people in the process). Fusing with Helios represents something new, something untried. But ending the game by basically replacing Bob Page (someone who wanted power) as the supreme autocrat with JC Denton (someone who doesn't want power) as the supreme autocrat goes against the whole thesis that power corrupts which is a major thesis in the game.
So . . .
Personally: Helios.
As an ending to the game: Tracer Tong.