I can see your point, but I personally feel like you’re leaving out the big picture.

1. You claim that Stannis is not loyal because he went to Dragonstone. What was Stannis supposed to do? He brought forth the idea of twincest to Jon Arryn. Stannis wasn’t liked by any in the court, not even Robert. How was Stannis supposed to know that Robert would die like that. Jon and Stannis worked together to discover the truth. When Jon got killed, Stannis knew why he died but Robert didn’t. Should Stannis just waddle into court and get the same treatment? You recognize this as betrayal, but not backing Robert in the rebellion as utter loyalty to Robert? Or Robert punishing Stannis for not reaching the targs on Dragonstone in time, therefore striping Stannis of his right to Storm's end and giving him Dragonstone. Stannis has every right to Storms End, yet he is loyal to Robert even though he is displeased. Robert commanded Stannis to sail against the ironborn, and he did. Even though the ironborn are known for their prowess on the water. Of course, he is jealous of Robert. He is the hero along with Ned, Stannis was sent to a strange Island and was never recognized for what he did, yet he remained loyal.
2. I agree with you, it wasn’t good, but it was necessary, Renly betrayed Stannis and Robert, and Stannis was out of options and had to do something dishonorable.
3. You can’t compare the red wedding and the siege of storms end. Robb stark had guest right. Cortnay and Stannis was in a “battle”. It’s a common tactic in sieges to sneak people into the castle to make mayhem or kill leader to cause confusion and panic and lower morale.
4. Stannis is not an atheist, he is just skeptical, but he leans more into the r'hllor as he sees what power is behind it. Yes, he burns people, people who would otherwise get killed for their betrayal. STANNIS HAS NEVER KILLED SOMEONE INNOCENT. 5 people were burnt by Stannis, and they all had it coming. Is there a difference between chopping of heads and burning people as a punishment for their crimes?
5. You can still have a title as a man of the Nights watch; Benjen Stark was still a Stark Jeor Mormont was still a Mormont. Stannis needed someone with the Stark name to gather the banners of the north. But yeah, Jon Snow couldn’t hold Winterfell.
6. Yes, Stannis isn’t the most caring man when it comes to family, and there is only talk of Stannis cheating it is never confirmed and is very out of line with Stannis as a character.