Rogue 09 said:
You cannot avoid all the glaring deficiencies and idiotic actions by Sisko. He played a major part of another culture's religion without any real argument (Said he was "uncomfortable" a few times, but pretty much accepted the role specifically for the power and influence it would grant him) which is very un-starfleet of him. Oh, and for those "He was still a God" people, he joined a group of aliens (abandoning his newborn child) whose only contributions to the galaxy are living in a hole in space. Yeah, they talked a lot about helping out Bajor, but when the Cardassians came about they really weren't into helping out that much, were they?
He also had one of his senior officers betray him, and then he couldn't catch him. Sisko was so incompetent he couldn't take that "great warship he built" (that was structurally flawed to the point it could destroy itself) and capture a single person who has nearly no resources. Your great captain, ladies and gentlemen! He finally did get him to surrender, but only by threatening to murder thousands of innocent people.
Don't get me wrong, I'm not saying that I object to some of his decisions. Most of the Sisko fans seem to be in that group because of the one time he tricked the Romulans into believing the Dominion was planning an attack. I should remind everyone, though, that he pretty much failed in every part of his plan in that episode and it was Garrack who actually saved the day.
Kirk had to deal with threats from both the Romulan and the Klingon Empires. For those who say he was a glory-hound or took too much risk in away parties, let me remind you that his crew included only 400 people. Most of these were specialists in fields as disparate as psychology, ship operations, biology, etc. He always took down the best group for the job and went himself so he could actively see and work with what was going on. Typically, the people remaining on ship flew around and did nothing, as they frequently lost contact with the away team. He always left the ship in the hands of one of his senior staff, usually Scotty. There was no diplomat on board, no councilor. His 1st in command was a science specialist, the only one with expertise in a field (Riker was a good pilot, Kira was a militia fighter, Chakotay was... well... indian?). Everybody else was needed somewhere and Kirk's job was to lead. Sue him.
Oh, and Sisko's girlfriend also betrayed him without him realizing it... but it's okay, because that's the type of person you want to marry and then immediately abandon. C'mon, this guy is a moron! What do you people see in him???
I will address your points in list format.
1. Sisko grudgingly played a huge role in an alien religion.
This is true, and it was very un-starfleet of him, but it wasn't actually violating any regulations and more importantly it wasn't necessarily wrong. The Prophets asked him to be their spokesman, and he agreed to their terms. He was sincere in his efforts, which we know because he eventually converted to the religion. It may not have been the Starfleet thing to do, someone like Picard would not have done it, but that does not make it wrong.
2. Sisko left his wife and child to become a God.
This we actually do not know for sure. The ending of DS9 was vague. I personally don't think Sisko had any choice in how that all played out or he would have chosen to return immediately. Remember, when Kasidy asked if he could return now his words were "I can't, not now." There is a better than even chance that those words were literal. He was, at that time, incapable of returning to Kasidy.
3. He had a senior officer betray him.
True, but that officer was assigned to him by starfleet and was already a Maquis at the time. This cannot be blamed on Sisko
4. Sisko was too incompetent to catch Eddington, even with the advantage of the Defiant.
Catching a skilled terrorist in their own territory among their supporters is difficult enough when you are looking within a single country or city, let alone a dozen or more planets. A powerful warship is not going to be an advantage at all unless you draw them out with a show of force, which is exactly how Sisko got him in the end. Frankly, the mistake was sending Sisko to go after Eddington in the first place. This should have been a task for Starfleet intelligence, but Starfleet answers every problem with "throw the nearest captain at it" no matter how little sense that makes.
5. The Defiant was poorly designed.
The flaws in design were relatively minor even if the results of these flaws was dramatic. It only took 2 weeks for Miles O'Brein to fix the design and actually make all the necessary changes to the Defiant, after which the design entered full production. The defiant class was a success.
6. Without Garrak, Sisko would have failed his attempt at espionage in the episode "In the Pale Moonlight."
This is absolutely true. Sisko knew that he was incapable of such sophisticated espionage, which is why he enlisted Garak. This is what a good commanding officer does. He used his influence to enlist someone who was capable of the task at hand. Garak said it himself: "That's why you came to me, isn't it captain? Because you knew I could do those things that you weren't capable of doing."
Sisko was a captain that did not subscribe to the normal Starfleet way of thinking. He certainly had his flaws, but he had several traits that I liked a lot that I thought made him an interesting character.
For example, Sisko did not see federation dogma as sacred. He was willing to honestly question his own beliefs and, even more importantly, he was willing to adjust his beliefs when they proved inadequate.
Also, he was actually tolerant and understanding of other cultures and peoples. He studied other cultures and when he saw something of value there he integrated it into his life. He read and understood the rules of acquisition, he sponsored a Ferengi entering Starfleet, and gladly participated in Klingon and Bajoran rituals. He even joined an alien religion.
Sisko is not your average Starfleet captain, which I find interesting.