It's really hard to pinpoint my 'favourite' protagonist. Firstly because many of the shows I've watched are great story, mediocre characters, but Secondly because it's genuinely hard to make a compelling, interesting character the viewers can appreciate. Anyways, here's my favourite protagonist(s). (Semi-spoilers? I don't mention specific events)
Eren Yeager (Attack on Titan)
Some call him generic, and that he screams too much, but I think Eren is one of the perfect example of the boundary between hero and villain, the meaning of true good and bad. He's neither good nor bad, just simply fighting for his ideals. But you all know him so let's not talk about him too much.
Koyomi Araragi (Monogatari Series)
Behind his rather antisocial, 'cool' personality, he has a real sense of justice, a pure heart to care for others. At first, I thought he was really bland and boring, just another pervy character. However, as the story progressed, I grew attached to him more and more. He truly cares about his friends, and sacrifices himself for them multiple time, even while knowing the conseequences it would bring to him. And all this stays in character with him. He isn't suddenly full of justice because of 'plot', everything he does just... makes sense for him. That's not to say he doesn't drive the plot forward as well. He's a tremendously remarkable unremarkable character, if that makes any sense. A perfect fit for monogatari, and it breaks my heart to see him often misunderstood as just a 'horni teen'.
Miyashiro Takuru (Chaos;Child)
Not 'anime', since he's from a visual novel, but still counts (yes there is a chaos;child anime but we don't talk about that). When the story starts, he is introduced to us as a 'right-sider', someone who is better thaneverybody else. He's extremely self centered and egoistic, and the readers are made to hate him. This already makes him quite unique and interesting. He isn't a generic 'relatable' or 'cool' mc, he's very arrogant and dis-likable. But we soon get to realise why he acts the way he does, and how he matures mentally from a child to an adult by the end of the story, learning how much he actually always cared about others, and that he's been lying to himself the whole time. Definitely my favourite character from the SciADV series, and one of the best instances of character development in any media in my opinion
However, none of them even comes close to SENAPI FROM TEJINA SENPAI
(She is hot)