Kirk is also a flawed character. So is Spock for that matter. Kirk is indeed heroic, resourceful, quick thinking and decisive, but he can also be impulsive and stubborn. He is intelligent and not a dumb jock like so many action heroes can be.
He can be charismatic and...he delivers great speeches.
I won't argue that Kirk and Spock have flaws but often they are not as apparent for me as McCoy's. They are often proven to be right in the end.
That being said I love scenes when their flaws are more apparent. For example one of my favorite Spock episodes is Galileo Seven when he realizes "logic" might not always be the best answer.
I think the films also do a better job than the TV series of growing both Kirk & Spock.
That being said I agree with a lot of your other positives of Kirk. Honestly when I started watching the show I didn't think I would like Kirk as much as I do because I am not a big fan of his character type, but there is something about Kirk that makes it work for me and I think a lot of that does have to do with Shatner's charisma & performance ( a similar character I am not a fan of for example is Hogan from Hogan's Heroes). I can understand why his men are so loyal to him because I believe in him too.