Since I read in the extras for the possibilities of a sequel it feels like the best ending to make a sequel of is Weaponized ending.
Liked Idol ending the most but its not sequel material.
That or make three different games with three different styles for each ending. >.>
I'm not sure about the programmer one, but the Idol one could easily be turned into another management type game, with two girls for the price of one, and maybe more added on as the MC could form a company exclusively dedicated to AI and Android managers. Whether it turns into an outright harem game, or one where the MC manages his relationship with his two girls while also dodging others that want to just use him to advance his career or stuff... There's really all sorts of possibilities here.
I can see the weaponized ending being used for an action or RPG type game. Doing missions and mercenary work to earn money, fighting off pursuers and android haters, and developing more complex technology and whatnot. Though it could also be twisted around into a stealth type game, where you have to ensure that you never go to "loud" and attract too much attention from the people hunting you.
The only issue I see with a sequel off of the weaponized ending is that it'd likely have a harder time maintaining the humorous tone of the original. I wouldn't personally mind a more serious game, but I have no idea how it'd work out. Of course, that assumes that the country they left actually cares that much about them...
No matter what though, the dev will have a hard time pleasing everyone, that's for sure. 'Canonizing' an ending for a game like this can make or break your fanbase. It's why big series like say the Venus Blood games or the 'Meister' games from Eushully are largely not connected between each other, to leave that freedom for endings.