I'm not the creator of the game but I will air opinions and my own predictions.
1. The idea of roleplay scenarios is a fun one though there is a small issue with your premise. Now I want Chainsaw to correct me if I'm wrong but according to previous comments, Regigigas will actually not be a robot but rather the organic creator of the other regis. Nothing else about that has been spoiled since wanna keep some surprises but she wont have some secret stored data because she ain't a bot. However, she could just build the holodeck because she is seemingly a roboticist.
Addendum: Wait no actually the Regigigas premise doesn't work at all because she's a sub-legend and the rotating ship scenes are tied to main legends people are for certain going to have so you would need a connection to either Palkia, Dialga or Giratina.
2. The idea for Palkia expanding space on the ship seems like a fun ship scenario. This has kind of lead me to my own question/curiosity. It seems Chainsaw has gotten into the pattern of adding some new rotating gimmick to the ship every update. Kanto is the Pregnancy Check and PokeGear, Johto is the AWC and Hoenn added the milk tasting. Is that a pattern you plan to keep up with? I know the ship is, in comparison to some of the other work you need to do for updates, not the most challenging segment of the game to develop, but that patterns seems like it could get a little out of hand. Though the complaint that you may be putting in too much content is barely a complaint that matters here.
3. I would be down for Jenny and JOY side scenes though I don't think they can be actual humans who have legendary pairings. This leads to another question... we haven't had a human girl for a side scene so would a side scene with a girl outside the main pairings lead to a PokeGear image. Again perhaps a little much in terms of work but that doesn't seem out of the realm of possibility. Perhaps compromise that by having it be one image for side human girls instead of two. Oh also the Growlthe thing specifically, I mentioned a detail about Arcanine that Chainsaw said gave them a good idea for a side scene so Growlthe a bit redundant if Chainsaw makes that side scene.
4. Fun ship idea and simple enough to be rotating. Like once they heavy pregnant that seems fun and they probably would want it then anyways.
5. First, there has been no brother sister so far only sister sister (nerd face emoji). Second, idk what you mean about mother daughter or father daughter but in the two ways I can infer what you mean one is "If its a Mew & Mewtwo thing or like Arceus & Giratina then maybe" the other is "Ew gross fuck no to that, the MC said he doesn't like incest much so he would never do that." Third, I see a sister x sister x sister scenario in Gen 5 that may become sister x other sisters in gen 8 but outside that probably not alot. I'm not really begging for more incest especially since it can get gross real fast but I can stomach a little if it has some sense to it.
6. Just wanted to ask how progress was going on Darkrai.