About the "message"?
It seems really more like the "deep" part is the game's originality, how it deviates from the norm. Otherwise, however, the actual game seems to be a pun in itself: Bitville, the "values" of bitville, etc.
Bits, pixels? Values (as in the values of data) for pixels, etc.
He goes on a mission to go... well, back to being bits.
But if you'd prefer a more mentally stimulating interpretation:
Jason believes life was becoming too "futuristic", technological, etc. He goes back... but he goes too far, way too far, to the point that the game is unplayable and the fact being that it isn't a game anymore, per se. Thus, should we realize, that change is acceptable; too much of the past may not always be a good thing (the extremists who oppose the direction of the future, perhaps?)
Remember also that Jason thought "this was fun", perhaps indicating that was the time in which pixels were "advanced" enough to make a game, and still be fun... going too far back, however, became a problem.