These characters are what I like and such is what makes them feel realistic. Characters with an obvious advantage, but also with an obvious disadvantage. Nobody is perfect.
Take X from Mega Man X for example. He hates violence- he’s a pacifist at heart, but he hates injustice more. In the endings of the various Mega Man X games, we often see him pondering about the ironic struggle of fighting in order to achieve peace between both humans and supernaturals, I mean Reploids. (This can also qualify under clash between their abstract ideals and reality). Such characters are good reflections of reality and if done right, can be role models. Seraphina from the Keeper series is also another one. Like X, she can appear very serious, but she will always lend a hand to those she believes in. For heroes that are a little wrong and villains who are a little right, well, I have (classic) Mega Man and Dr Wily.
What characters I don’t like: flat, one-dimensional characters. Those with no weaknesses or no strengths. We need nuance! And I don’t like romantic options just for the sake of having romance options.