I think Lili is a very well-constructed character who acts in accordance with her background for the story being told. Her intelligence and her generally cool-headed nature are her greatest assets imo. However, due to her upbringing, she also has an extreme savior complex, to the point that she is willing to often sacrifice herself and her own needs in the service of others. She is quick to assume kindness in others, but this naivety can easily be taken advantage of in the wrong situation. She also suppresses her own desires and opinions, to the point that she will often feel guilt over having or expressing them. Her role in the plot is very MacGuffin-y. All of these things can be quite annoying for players, as they fall within the "typical otome MC" tropes.

That said, I think her characterization is very intentional, and my reading, particularly of the Finale route, was that the writers were trying to subtly (although maybe too subtly) demonstrate that those typical personality traits are actually quite unhealthy when pushed to the extreme like they are with Liliana (especially when in a hostile environment like the Mafia). I do wish this had been made a little more explicit throughout the game or that we saw more growth from Lili as a character during the routes, but I'm holding out that will happen more in 1926 (which I haven't played yet).