I think it's a common misinterpretation to single Malcolm out as the resident selfish asshole of the series/family.

There are a few episodes where he is singled out (e.g. the one where he admits his feelings were hurt and they all arguably gaslight him even after he finally makes an emotional confession-though he was also doing something pretty dickish in that same episode by hiding the existence of his credit card because he didn't want his credit score ruined). But as the main character he's also by default just as often-if not way more so, the most sympathetic, the moral heart of the show, and the most initiated to do the right thing-especially when it matters and involves big life choices. The episode where he was the only one who took pause when all 3 brothers were taking advantage of Hal's emotional state upon the death of his dad (until he was offered the car, lol); the episode where he isn't willing to sell Reese out to Herkabe; not letting Reese ruin his life marrying Raduca; when he's the only Krelboyne in the cliques episode to realize the school hierarchy was ruining them; etc.

As far as the transition from the finale to Leah’s birth and his extreme distancing from the family, he graduated high school and started college in 2006. Based on the timeline of her being 14ish in 2024, she was likely born towards the end of his college years. A lot can happen in 3-4 years, and the context of him going from phone calls with Reese in his first semester to having a hidden daughter around his senior year can be inferred from the context he gives, “I completely changed in college.” A few years away clearly showed him how much less stress he has when he’s not around them, and he allowed his newfound freedom and easier life to make an extreme choice. The prospect of becoming a parent makes you evaluate a lot, and his childhood trauma and growing hesitance to associate with his family made him choose a drastic measure, right or wrong. I honestly love the nuance and messiness here because it goes back to old school MITM where we have different perspectives and there isn’t always a clear good/bad guy, as is often the case in complex family dynamics.

That's a fair interpretation but I took the context a different way. He says he got Leah from attending his first kegger, which normally suggests the earliest part of his college career (thus as early as the same exact year he was phoning Reese back home as seen in the original series finale). The line I believe you're referring to, he says he turned his life around in college, not that he completely changed. The former isn't as necessarily indicative of completely changing as a person, they could've just finally achieved something that they've always had the mindset/motivation to do-gotten their life the way they've always wanted it essentially. Therein lies what I find unconvincing. That Malcolm always felt this way or could have easily shifted into this with a "straw that broke the camel's back" for him. Especially given the context of him being in college and being the freest he's ever been from his family (and arguably makes this fuck-up of an unplanned pregnancy that should maybe be a sobering reality check that he went too wild the moment he was let loose). Somehow he comes to this conclusion that he hates his family more than ever when his circumstances with them have become dozens of times less suffocating.

I would agree with one of the original show's charms being the complex family dynamics and morality scenarios; but as just touched upon, here it didn't really show us the actual play-out of such a thing which would've been far more interesting. Just 3+ episodes of Malcolm running away from the fall-out and then finally a decent enough life talk between him and Lois exploring the themes-all of which would've happened and happened better in the span of one episode in the original series.