I say it's this order:
Warden -> Inquisitor -> Champion
Now the warden may be my favorite, but that's not why I believe this and I also want to specify that this is only if you do everything in the DA:O series and expansions.
So to start the Warden is a Warden, tainted blood, heightened senses, all that good stuff you get for essentially giving yourself blood cancer, but the Warden could potentially even "unlock the secrets of his/her blood" in the Warden's Keep dlc where they get special and powerful abilities due to their tainted blood. This would no doubt give them a strong advantage over others, more so then their normal Warden abilities. Also, in a less lore specific manner, the Warden can get 4 freakin specializations, that's a rather distinct advantage over Hawke's 2 and the Inquisitor's one.
As for the Inquisitor, I'd say they are the strongest if the warden didn't get the special abilities, cause the Warden's other strengths are mainly focused at Darkspawn and not other people, where as the special blood abilities are a general "steroid" of their strengths. The Inquisitor's abilities are fade focused as well, not really at other people, but as we've seen certain abilities can be gained from the fade to be used against everyone.
Finally the Champion, Hawke, the normal everyday leader with no special strengths besides being able to lead people for some reason. By far the weakest of the three, sure they can get 2 specializations and the Inquisitor can only get 1, but the Inquisitor also has fade abilities which carry greater weight in a lore based position and only even out in a game based position. Not too mention Hawke has the least amount of experience in basically everything once all the stories are through with massive amounts of down time in between their little city and forest excursions.
So yeah, Warden -> Inquisitor -> Champion.
EDIT: I didn't mention army sizes cause that's an obvious answer to literally everyone who's played the games. that's not longer a question of use the strongest protagonist but a question of "all of thedas, just ferelden, or some people in kirkwall." So yeah, fi that's what you're basing your decisions on then there's no point in saying anything cause this answer is as obvious as it gets and is not what the thread is asking.