Nothing ever came out of...
...the OBVIOUS fact that it was Sloan who was in the car accident that killed Sydney's mother? When we first see the newspaper clipping of the accident, there's a picture of a man who caused the crash and it's SO OBVIOUSLY SLOAN!!!! But Sydney doesn't realize it.
Then later when she finds out that Jack was being investigated by the FBI agent Calder, his widow shows her a picture of the SAME GUY from the crash. And again Sydney just thinks it's the guy from the crash who was after her father for being a spy. But then it's cleared up by the fact that they were actually after Sydney's mother, then it's never brought up again.
And it turns out that Bristows and the Sloans are actually good friends, good enough that Irina and Arvin could have an affair together. When they hypnotize (or whatever they did) Jack talks to Sydney (who's supposed to be her mother) about doing something with Sloan and his wife, and Jack says he knows she doesn't like him. But she says they're friends so she puts up with him.
Anyway, that's just always bothered me. It's Sloan in the picture. OBVIOUSLY. I know they did a lot of rework as the series went on. It seems as though JJ Abrams had the idea of Felicity going off for a summer and working for the CIA and coming back as if nothing happened, but that was all.
I love the first two seasons, and I like the third season. I hated Lauren so much, but the 3rd season was really good.