"12 and 5'0", he only grew like 7 inches over seven years" are you even talking about reese anymore, or the actor? because the show can not really affect how reese ages, that is how the actor ages. It is not like they can force Reese to look super tall and tough looking, if the actor doesn't grow up that way.
basically both Reese and Malcolm went from being kids to young adults during the course of Malcolm in the Middle. So really when they could not predict either of the actors futures from the beginning of the series.
So the show decided to make Reese no longer a bully, and Malcolm not as smart as we taught he was, I think that was a good decision, otherwise many people would have been bored with the show, and I doubt it would have has a 6th or 7th season, so probably that why the storylines shifted in Season 5
Oh and Justin is just small? not when being compared to Frankie, Frankie never seemed to grow, lol. I saw Frankie in "Stuck on You" last night, and he plays himself as the teenage boyfriend of the superstar Cher. Now that was a little creepy, but funny as well.
Cher [to Frankie, while in bed together]: "Go to bed. You have a geography test in the morning."
lol