Wait So Long

I think the previous comment hit the nail on the head. Adding to that

I think it's about a guy who loves a girl and has always been there for her despite the shitty guys she dates, and all of the bad decisions she makes. She always comes to him with her problems "And you call me in the morning with your troubles. "Takin' it downtown every night" and he gives her advice which she ignores until it's to late. Then when things fall apart she recognizes he was right "and you know I'm right" "Any afterthought rose to recognition". Then she goes on to repeat the process, choosing bad relationships over a healthy one with him. He's gotten to the point where he's content with his role in the relationship because he knows she won't change, and see's she's too damaged if she ever did.

Even though he knows they'll never be together he still loves her, and will continue to help her even though it's become a "bad habit" because he realizes that his only problem is that he's "doomed to repeat" helping a somewhat hopeless cause.

He realizes that his biggest problem is that he's helping a lost cause, but is willing to sacrifice his help because her problems outweigh his.

Overall it's about him acknowledging the situation he's in, knowing it's not gonna change, and being selfless enough to stick around to help because he loves her, even though she'll never reciprocate.

I may just be seeing what I want to see in this song because it illustrates to a T a relationship I have with a friend, but nonetheless it's a great song with great lyrics.