I don't think it's a coincidence that GRRM made Jon the 998th commander. I'm almost positive that the 999th will be Ser Alliser Thorne. So who could be the 1000th? For a while I believed it would be Jon Snow again but after the season 5 finale I believe it will be Stannis Baratheon.
I know this sub is split right now on whether Stannis is alive or dead but hear me out. GRRM does a great job of adding realism to his stories but he is still a story teller and most things he does has a purpose. Killing off Stannis at a that moment doesn't really have one. The guy saves the Night's Watches butts and camps with them for a while before making his way to Winterfell. Losing everything and then dying to the woman sworn to protect his brother is tragic but feels unsatisfying.
So why does it not fit despite being almost a perfect Greek tragedy? Because it doesn't make sense when looking at the rest of his story. 3 of the 5 kings in the War of the 5 Kings have at least 1 POV character to explain what they are doing. Stannis being one those shows how important he is. If the whole point of his character is to be a huge underdog the entire war and then wimper out to get Melisandra to Jon then that's weak because he really hasn't done anything since Clash besides save the Night's Watch. The focus on this man and GRRMs making him such a liked character makes me think he has a bigger role to play yet.
But what makes Stannis so likable to begin with? I think a lot of us see him as a hero of some sort because he is a man of values which is rare in this story. He's just and uncompromising when it comes to what he believes is right. He paid his dues and knew his role. And unlike most of the other kings he has the legitimate claim to the throne. The problem is he starts losing his way by listening to the Red Witch more and more. This leads to his tragic fall in the show when he sacrifices his daughter and loses his wife and army in the process.
So why must he live on? Because Stannis, more than almost anyone else, is fit to lead the Night's Watch and right his wrongs. He lost his honor and his way because he was too focused on what he deserved but he is the perfect man to bring back honor and renown for a group who has become known for being made up of criminals.
One last thing to consider. Stannis has no wife, holds no lands, has no children, wears no crown and has no glory.