I never thought it this way, it totally makes sense. It is a risk, for sure, especially for solo projects like this one. Still, I am of the opinion you can do a better job and still have a likeable MC with a fleshed out personality. A good example is Tomoya, the MC from Clannad, another excellent japanese VN. He is on the safe side (kind, caring, likeable, etc) but with some flaws and quirks that make him interesting enough.
By the way, I forgot to talk about the girls in Eternum. I actually didn't like the "main" girls that much (you know: Annie, Penny, Dalia), but god damn it! I love Luna, Alex and Nova! Oh, and Calypso, too! They have very good arcs and development. I even got emotional with Alex backstory.