There are so many fun accidental and not so accidental implications in MitM when it comes to Malcolm and Stevie's relationship and I feel like there's not enough acknowledgement of how close these two actually are.
Malcolm acknowledges out loud every new piece of clothing that Stevie gets.
The first thing Malcolm thinks of doing with some extra money is to buy him and Stevie lunch.
Malcolm and Stevie play chess via e-mail on the daily basis.
They are so supportive of one another. Malcolm's attitude is especially fascinating, because he often is easily dismissive of people's acomplishments, especially, if he finds them "uncool", but he is very outwardly happy for Stevie.
Malcolm doesn't like upsetting Stevie and often chooses not to bring up things, which he wouldn't have an issue bringing up with other characters.
Malcolm will also most of the time immediately try to apologise/make up for his wrongdoings to Stevie — again, this is something that he struggles with when it comes to other characters.
Malcolm spends most of his free time with Stevie, to the point in which his brothers (esp. Reese) just keep bringing it up.
Stevie just really likes hanging out with Malcolm, even if the other boy is busy with something (see: Malcolm's time as a magazine editor; Malcolm playing chess in the park; Malcolm running the computer simulation). They probably really like parallel play.
Malcolm really likes Stevie's personality, even though he's often subjected to Stevie's sarcasm and antagonistic behaviour. What's more, Malcolm looks flabbergasted at the insinuation that he would find Stevie abrasive.
Stevie also really likes Malcolm's personality, even though he is quick to point out when Malcolm's being annoying.
Outside all the gags and jokes, and whatnot, it really might be Malcolm's most important relationship.