I think Kodaka has a distinct favourtism regarding Naegi compared to every other protagonist in Danganronpa.
Naegi is the only protagonist to not only have a fully-canon love interest, but his love interest is also alive and well *AND* he has two other semi-canon alternative love interests whereas Hinata and Saihara only get one heavily implied love interest who's dead
Hinata and Saihara have actual flaws that bite them in the ass by the narrative, especially the former. Naegi? What are his flaws? When was he ever in the wrong? When has he been called out for his mistake or error? None
I was indifferent towards him at first, but overtime I ended up starting to dislike him after being numerously exposed to him being painted as some ultimate gigachad by dudebros and harem writers on numerous social medias and the more I think about his rehabilitation of The Remnants of Despair before Izuru/Junko came to corrupt it, the more I realise just how terribly flawed it is as he is willingly to erase all of their memories (the same exact way Enoshima did for our supposed paragon of virtue and morality) at their time at HPA, meaning they are also forgetting the two figures who unified them in the first place; both their class rep (DR3!Nanami) and their homeroom teacher (Yukizome) who are infinitely more empathetic than he actually is. And what would he do if they saw the current state of the world alongside the changes in their bodies without their memories as RoD?
Fuck, him rebuilding HPA alone makes me went from being indifferent, to disliking him, to having him as one of my least favourite characters in the entire franchise. People LOVE bashing on Nanami for being a mary sue but ignore the biggest gary stu that is Naegi Makoto
You're absolutely right, Makoto has more focus and "achievement" for lack of a better te rm than anyone else. No flaws, no weaknesses, never called out for anything, at least not properly. Compared to Hajime and Shuichi, who we saw undergo a lot more change and growth, as well as having clear character flaws that clearly bite them.
There's also a distinct favouritism towards him I've noticed in the fanbase, it's disturbingly popular, especially on Reddit, for Makoto to be some sort of casanova pimp with about 8 wives and even though I don't think Makoto has all that much character, that depiction contradicts the very small amount of it he actually has. Also, polygamy is objectively a bad way to live, so add that on too.
Don't get me wrong, I like the concept of characters who are brave, noble, valiant heroes who embody hope and are the last hope of the world, but Danganronpa is a gritty murder thriller about people forced to kill each other to stay alive, a protagonist like that doesn't really fit.
And yeah, he's also...kind of a hypocrite like you've said and a bit of a dick as my good friend Yuki from back in the day has said. I get that he's the protagonist of arguably the whole series minus V3 but...yeah, he kinda just sucks.
Also, I'm so sorry it took me so long to respond to this, I've just been a bit burnt out from Tumblr the past month or so, but I think I can get back to speed.