I'm not talking in the short-term sense, as there's no doubt the ending was the one thing most people remembered about the game. But in long-term, it sort of put Telltale in a bind when it came to continuing the story.
You have to view these games almost like an interactive TV show (an aesthetic approach Telltale themselves confirmed when they referred to the next series as "season 2", not to mention the "Previously on the Walking Dead/Next Time on the Walking Dead" clips seen at the beginning and end of each episode). In TV shows, the lead protagonist doesn't usually die. Not at the end of the first season, anyway.
I think it's somewhat safe to assume the Telltale writing team is probably jumping through the same hoops we are in terms of what to do next. We've speculated almost a dozen different ways about who the lead in season 2 could be, and every idea, no matter what it is, has come with its share of problems.
I know that even suggesting this out loud will get me lynched, but I can't help wondering if Telltale will reveal story events from Lee's bite onwards was just a nightmare Clementine had, just to bypass all the headaches they're probably having to go through in story sessions. To be honest, I wouldn't blame them. :o