The short version is that the project was gaining traction and growing larger than was originally envisioned. It started out as sort of a one-man-project spiritual successor of another game that never got finished, and the dev was just sort of making it up as he went along. As the project began to grow, he realized that if he kept up with the improvised approach he'd started off with that the game development was going to turn into a serious headache, with cascading bugs and graphical issues. Between that and also bringing on some other team members to help out, they needed a more elegant and unified approach to the coding and project workflow, else the project was going to end up floundering and dying due to development strain and multiplying bugs.
Ino gave consideration to waiting a few more releases to do the overhaul, but decided that ultimately it was going to be better to tear off the bandage early than do more development the hard way and end up with a bigger backlog when it came time to do the change over.
It was also an opportunity to re-approach the graphics in the game, which originally were basically just Vanilla RPG-Maker assets that were square-peg-round-hole-style being made to work with this game to a sort of "Eh, good enough" standard. They swapped to Parallax mapping with custom assets and custom sprites with variable heights and animations in order to better suit the game's aims.
Basically it was a move to make the game have better potential as a finished project, at the cost of short-term loss of content.