A New Frontier is NOT Season 3...
Yes, you read the title correctly. I do not think ANF is the official season three of The Walking Dead, but a DLC connecting to it.
Let's start with the title: The Walking Dead: A New Frontier
I hardly have to mention that the past two seasons have always been titled according to which season they were (The Walking Dead: Season 1, The Walking Dead: Season 2). But ANF has it's own distinct and individual title aside from these two, which at first seems confusing. The only TWD video games out there with titles unique to their story were the DLCs: (The Walking Dead: Michonne, The Walking Dead: 400 Days). This suggests that A New Frontier is just so special, it deserves a title of its own, a title for a DLC. Even if you go back to the homepage and look up the game, Telltale makes no outright call out to it being Season 3, only ever A New Frontier.
This could also very well explain why Clementine had such a limited role in the game—it was a story apart from hers, apart from the official seasons which focus on her specifically; a DLC shedding more focus onto a different aspect of The Walking Dead universe, that being, the New Frontier. This also explains why we only see AJ in flashbacks and never directly in the game, because he plays more of a role in the official Season 3 to come.
But why would Telltale make ANF a DLC in terms of the overall story, instead of just another season?—because the New Frontier will play a role in the official S3's story and in order for them to fully play that role, they have to have the general audience introduced to them already. Clementine already confirmed that she will eventually return to New Richmond and meet with the Garcias again.
Episode 5 (after Javier gives Clementine her haircut)
Javier: Your dad ever teach you about Baseball?
Clementine: No, not really.
Javier: Well, you come back, and I'll tell you all about it.
Clementine: It's a deal.
I could be absolutely wrong about this theory, but tell me what you guys think. 
Comments
It's season 3.
It's not Season 3.
Yeah....
Nah...
Heh, I hope it isn't.
A New Frontier
Season 3
They have different ratings, age restriction and content warnings.
It's classified as Season 3 in the game files if I recall correctly. And developers have called it Season 3 multiple times.
Sorry bud, but this is Season 3. That doesn't necessarily mean we won't get a Clementine season though.
I'll let you figure out which stage you're currently on...
Alright then, I guess I was wrong. It was a thought worth writing about, though.
ANF was a bungled mess telltale slapped together which quickly fell apart despite trying to put bandaids on it to the point where they rushed EP4&EP5 out to move away from ANF as a whole to make Clementines legitimate continuation.
Denial is not just a river in Egypt
Well look at the product we got. An excessively rewritten installment with frequent writers and workers leaving mid season or leaving the project with a revolving door of various writers which showed blatantly in a negative way. This is what telltale intended to be S3 only to become a aimless series with no direction or passion put into it with telltale trying to salvage what remained of the series.
I mean, it is bad I agree. But it's still confirmed season 3.
I'm not disagreeing I'm simply saying they meant for this to be a legitimate continuation only to produce what we got.