Um, so you propose to change only pictures (naruto/naruko/kushina) and dialogues without changing the actual character?
Well, that is what modular design is about, correct?
You make sure that the ciore fuinctionality works, and where you know it needs a bit of work, you make sure it works in version 2, and as soon as you go into release, you go to version 2, and polish up.
But yea. I figured, since you talked side characters, and minor chracters, you would not mind if I treated everyone as a minor chracter first, and then when I had some ideas, reworked them.
For example, the easiest way for naruto would be:
version 1: male naruto is chained to a bed. Female naruto serves as a minor character, that can be wined, dined, and most enthusiastically fucked. ( minor quest)
version 2: we know of the existance of naruto mama. Naruto mamma wants her baby to have it good, but she herself has a few things left to do. So, in effect, female naruto, when we trigger the overeating, gets exchanged with mamma naruto. Stats, abilities and so on stay the same, just a bit more scripted replies, and perhaps 2-3 quests.
version 3: Mamma naruto becomes dateable. Female naruto has passed his punishment, and becomes male naruto for the first time in ages. He only uses it to pee against thjings, and then changes back, because he liked being female. Tsunade gets wind of what is happening, and gets the player for some research into the condition ( 2 medium quests added, 4 minor quests.
version 4: Tsunade wants to implement a force prism, that should lock off a tiny bit of narutos chakra, and allow naruto mamma to no longer use her sons body, but use one of the shadow clones, to form like her. Major story is added, major quest, a medium quest, and two minor ones, and at the culmination of all of them, Tsunade manages to unlock the chakra prism, with the effect that Mamma naruto manifests. what follows is a foursome, with naruho, mamma naruto, and tsunade, who enjoys the perverted nature of it, and would very much like to see more endings like this, with everyone just ending in a peacefull orgy. Female naruto, naruto and mamma naruto are now dateable and can be taken in the party, each with their fully fledged natures and topics.
Thus, do what you want inh each version, but make sure if you upodate the naruto storyline, you update it till the stepping stone. Thus, if you update, it does not feel incomplete, but instead makes sense.