Allow me to go down the list.
Picard As a character seems to be the most well rounded, competent and facinating. He is a scholar by nature, an explorer by passion and a warrior by circumstance. Perhaps because Roddenberry was no longer as directly active after the horrible first season of TNG Picard was far more of a captain than kirk.He was talented and knew how to get the job done but his greatest skill was picking and managing a crew that knew their jobs better than he did and delegating well. Picard is simply a well rounded and interesting character who does not insist upon or overstate himself. His charisma makes him a great leader but he is humble enough to know that it is only because of his crew that he can accomplish his missions.
Sisco a close second. He is a bit more flawed than picard,wise but without the added edge to that wisdom age produces. The whole messiah complex theme of the show never seemed to affect the character in a way that made him seem more like a man trying to do what was right. He simply wished to fulfill his duty to the federation and do right by his son. I imagine him being much the man Picard was at his age only with the lessons of fatherhood further tempering his disposition.
Next would normally be Sulu simply becasue he is cool but in the spirit of this thread I'm going to choose the next 'expected' captain in line and say Janeway. Now I love Strong female role models. Cat Cora ranks up there almost with Tolkien as a role model. Still She seems to insist upon her strength, especially in the early seasons where they deal with the chauvinistic aliens. Yes sombody needs to punch them but the best way to deal with it would simply have been to insist they deal with her as the ranking female and then force them to accept it. Don't insist, don't wear your ovaries on the outside, just be more human about it. I admit as a character she mellowed out a bit but then she just got that 'Xena implied bisexuality/Lesbian' thing writers of the time seemed to love and while I usually adore such a thing (God... Priss from Bubblegum crisis..) With her and Seven it never fit. She seemed like a good character with a fitting actress that simply fell prey to all the male writers either not knowing how to write the role properly or watching the warrior princess make out with Gabrielle too many times.
Until Enterprise Kirk would be placed here at the bottom. The man is incompetent, selfish, self centered, womanizing, immature child. He refuses to accept defeat past the point of commendable bravery, He insists on trying to do things himself even when he is less skilled. He has an obvious prejudice towards alien races even if that seems to be the norm at the time. I think Shatner did a poor job of playing the character but I don't think it was a character worth playing. Under This is, I feel, In part due to Roddenberry as it seems Star trek got more well rounded and complex the further away from him it moved. Kirk is the obvious exemplar of this because, well lets face it the man is an antiquated cowboy with plot armor going around in deep space seducing green chicks.
And yet sadly recent events have made a whole new bottom of the Barrel, Archer. I can't fully blame the actor or the role as both may be better in a setting that is not so utterly painful. Still Archer seems to be Kirk sans the interesting character development. The man Is bland as a piece of white bread dipped in water. For the most part it seems that his personality simply molds itself into being a reluctant or eager voice to back whatever course of action ends up taking place. He does almost nothing to galvanize his crew and aside from some kirk-like prejudice against Vulcan early on shows nothing of any particular note at all. At least Kirk had some suck to complain about. Archer is apparently suppsoed to be some massive historical figure, a galvanizing force to some inter-temporal civil war that makes him out to be a messiah or something. He fights it, he goes along with it. But its hard to see how he can draw together anything other than the fact that he is there at the time. He doesn't even have the bad personality to bash, he has no personality at all.
Thats my assessment anyways. Feel free to argue or point out why I am wrong if you wish. Its late and I'm tired but I felt I had to post this.