There's progress being made but there's not a single person here that'll disagree that the project was mismanaged, because Dark Cookie is figuring it all out as he's going along. Whenever DC "finishes" something, either he, Captain Sploosh or Stray error get a new idea, and they go back and implement them into the story. When they started doing that, they realized that Dogeeks coding was a mess. An example of that was something along the lines of Dogeek naming files "Booger Aids" that gave no indication of what it was.
So now you have them adding and expanding onto the original story with new animations and cutscenes, while reworking the entire code to not only straighten everything out, but to make sure that the new stuff they're adding and updating, works with older content, but still looks comparable art wise. It's a mess to be sure, but this is what happens when you don't have a solid plan, or change said plan from the start. Another example is the aspect ratio that required every single background to be reworked and every single character had to be repositioned on the screen. Some of the characters like Jenny have files in the thousand plus range, with the main character dwarfing that.
It's also important to remember that this was never intended to be an actual game, and that DC was just playing around to see if he could make anything worthwhile, while learning RenPy on his own.
It genuinely sucks that the game is in the state it's in, but there's nothing anyone can do about it.