Mahomes has more natural abilities as a QB than Brady, but tbf to Brady, he's never really been that type of QB. There's a reason Brady was a 6th round pick; coaches want a freak of nature they can mold into a QB, but Brady wasn't really the finest clay in that regard.
Brady has high game IQ, though, and he had really good longevity, which people for some reason like to underrate when they compare young people to Brady. Brady's regression was much kinder to the point that he never really was at a point, even at his old age in the mid-40s, where it straight-up looked like it was over. Compare him to Manning, where, despite Manning winning a SB in his final year, looked so far from his prime that his ring that year felt like everyone else won in spite of Manning's poor performances.
Another thing, which comes with age to an extent, is that people wanted to play with Brady. Gronk came out of retirement to play with Brady, so the charisma and the winning attitude made him someone that could keep having elite players in his old age. Won't value that too high as that's pretty subjective, and unfair to compare a young QB to, but it's still something.
Yeah I think that's what people miss in the comparison. Tom Brady basically had 3 HoF careers. Mahomes is fantastic, but we've yet to see what he looks like when age starts picking up.