Jesus christ, I think you put more thought into this whole comment than I have into full updates!
First off, I LOVE this idea, the Dittos all following the MC like he's their lord and saviour is a hilarious idea, them hiding all over the place and watching over him could lead to a lot of funny situations too.
My only problem with this is that I have no idea how I'd implement it into the game, maybe if I set it up as a side section, the Dittos invade the ship in after a chapter and get dropped off before the next one starts.
I'm going to add this whole comment to my notes and come back to it later, I'm sure I can do a lot with this idea but it'll take some time for me to get my thoughts together and make a plan!
Also I would like to remind everyone that I asked for suggestions to stay simple, I'm fine with this one because Zander has been a regular commenter on my game, they've earned this one.