The central mechanic of upgrades being linked was pretty cool, but not very well communicated. The twist with the final character's "sacrifices" was VERY cool, and genuinely felt a little brutal. It would be nice to have a little more automation, or at least a way to buy more than 1 upgrade at a time, but I could see that being a deliberate design decision to make the player more willing to give up control of the characters to Atraia.
(the rest of this is a plural person rambling about their interpretation of this game's story)
I think the implication of this game is that it's a view of a plural system (probably one undergoing final fusion) through the lens of an incremental game; each character is linked in subtle ways, and it becomes increasingly complex to try to manage every different thing for every person. Some of them have entirely different styles, but it's still fundamentally the same thing -- and there's always that little hint, that idea in the back of your head that it would be so much easier if there were just less to think about. That if these people are so similar, and already sort of connected, isn't it better to just have one less person to manage?
All you'd need to do is.. have that person give up their originality, their individuality. And every time someone gives up, every time someone stops being whatever they were and becomes something more like a normal person, there's a little less strain on everyone else; it gets a little bit easier for them to carry on... and a little more tempting to stop being the narrow-minded things that they are, and be something more... normal, I guess.
Gah. It's technically recovery, but it's still tragic in a way, and I think that's depicted really well here, even if that wasn't originally the intention!