At the very least, if a phased approach is taken, focus on reaching a distinctive stage that permits a full gameplay experience as far as progressing the story. Then, if you decide to revamp some aspect, you have a "complete" story/chapter to work within. That also gives you distinct milestones to follow. So, for example, you could spend X/X time in a year working on producing the next chapter, Y/Y in a year working on code revamp/upgrades, Z/Z in a year on bugfixes.
Personally, the things which always make or break a game/vn for me is: replayability. Having a function which allows the replay of certain scenes is one way to make a game that I have "finished" interesting to come back to. Alternatively, if there are different endings based on "paths", then it can appeal to the completionists (myself), and the folks who like trying different flavors. Being able to play the game, and revisit scenes is great too.