The obvious counter-example is iron man, especially in the films.
More in the comics, I would say. In the films he only has one self-modification: the fusion device in his chest, and that is more of a medical device required to keep him alive than an actual transhumanist augmentation. In the comics, Stark has to continually modify his biology to keep up with the enhancements to his armor/fight more powerful villains.
Actually Captain America is perhaps a better example. He becomes a super soldier not by accident, but by volunteering for an experimental human-enhancement procedure.
I just watched this, a very pretty version of "don't try to make yourself different, just accept who you are", and I realized that self-directed change in fiction is a worthwhile topic.
What I'm looking for is stories where main characters change themselves in ways which are basically improvements-- getting beyond the usual human is a plus, but for purposes of this discussion I'm including any significant positive change.
Another big plus would be the character needing to learn which of their goals make sense, and which methods work.
**ETA:** That was a bit of a stub-- HPMOR is partly about Harry and Hermione changing themselves, generally for the better I think (I've only read it once). It would be interesting to see what happens if Quirrell decides he needs to upgrade himself.
*Stranger in a Strange Land* is an interesting partial example-- the Martian language is presumably an upgrade for the human race, but it was developed by and for Martians, and needs some modification.
A *lot* of relatively recent fiction has people learning martial arts. I think appearance makeovers (typically for women) have become less common. I don't think there's a lot of fiction about appearance makeovers for men-- *The Stars My Destination* has one, but it's offstage. It wouldn't surprise me if *The Count of Monte Cristo* (frequently referenced with TSMD) has one.