It took me a while to actually play the game after seeing your comment first, and I can agree with parts of both your POV and Breecer's.
Personally, though maybe this is just my bias for character design, perhaps Eugene's personality wouldn't be received so poorly (at least by you and those who agree, which I say with no judgement) if his backstory as a mass-fixated apothecary were conveyed at the beginning before his conversation with Phil, and if he were visibly designed to look more dramatic and opulent than he does now. A grandiose personality with a Joe Schmoe outfit creates dissonance, but if he looks the way he acts, then you know what you're in for, y'know?
But, of course, redesigning him or all the other NPCs to look more maximalized and fantastical is a lot of work to have to do, especially with animated scenes and all the different physique alts. So, unfortunately, that's likely not very feasible.
I may make this the focus of a separate content, but maybe Eugene's personality (his overwhelming forwardness and such) would be softened if the game had a little more "breathing room" with its text. Instead of a constant stream of dialogue and action outside of the growth scenes, taking time to describe things and give space between dialogue might make it feel less intense to players?
I don't always need the protagonist to effectively be a self-insert, but even then, some players are more proactive, dominant, forward with their desire to grow NPCs. I wouldn't say Eugene is "unrelatable", just relatable to a different demographic.
As for his desire to help the town being "selfish" and not exactly from a good place, I can again see your point - not that that's necessarily a bad thing, writing-wise. It's all about the framing and how the material wants you to take something. But, you could choose to take the growth Eugene provides as a kind of symbolic, meta-textual parallel-ism (to use big, fancy writing words). Eugene is helping these people get what they want, and what they want is just being tied to growth; the growth is just a representation of their progression for their route towards happiness and fulfillment.
And regarding "wanting more" from a VN but it feeling like an "average FA growth story", I also see your point there. On one hand, it's cool to see the kind of content and scale of an average FA story being elevated by using the VN medium to convey it. At the same time, when VNs are inherently a different medium than written stories, it's kind of convention to give them, and thus to expect from them, more substance and consideration. It depends on who you ask, I suppose.
Sorry if drudging up such an old comment is unwelcome, I just wanted to give my two cents!