It sort of felt like there was a lack of true consequence for some of the "major" story choices. All you get for abandoning Lilly is a brief mention of it by the stranger in Ep. 5. It seems like a lazy, contrived way for supposed "major" story choices to have real consequences. What about lying to Hershel, or shooting Jolene? Were those choices even mentioned at the end of the season? (If you tell Lily about Jolene, the game says "She will remember that", but she never mentions it afterward, even up to the point where she leaves the group). There's also no consequence for how you respond to Lilly's offer to go with her on the RV or not, nor is there any real consequence to surrendering or keeping your weapons for the confrontation with the Stranger, despite being listed as one of the "Big 5" story decisions.
There are so many loose threads that never get tied up. Is Kenny really dead? What happens to Vernon and his group? What happens to Molly? What about Omid and Christa? Do they ever find Clementine? ...My ultimate hope for these is that Season 2 will tie in with the choices of Season 1, and we'll get to see what happens to these people. ...Although that may be over a year from now; the wait is so agonizing...