Micah breaking up with Penny was genuinely one of the best things to happen to Penny. Not just because it freed her up to meet and be with Shepard (though that's definitely a perk), but because it was a wake-up call for Penny and the ways she treats people.
I wouldn't broadly label the ways Penny treats people as bad, but they can be read as inconsiderate. She famously says that she doesn't have time for too many people in her life, which can lead her to cut off people who might otherwise be interested in getting to know her. She is invested in Simon and his adventures to the point of exclusion throughout Carry On, something implied to have been true since they met in first year. She tends to steamroll rather than listening first to others' opinions and desires (something she does to Simon, the person she cares most about). Her sense of other people's boundaries is maybe...less developed. And, when it comes to Micah, she keeps him at a geographic and emotional distance.
The evidence is mounting for autistic Penny Bunce.
Micah calls Penny out for all of this when she pops up without warning at his house, expecting him to be a.) still in a relationship with her, and b.) happy to see her. He is neither of those things.
Now, we only have Micah's word that he told Penny multiple times that their relationship was over. We don't know how subtle or forthright he was every time he brought up the topic. Penny is blunt by nature, and she responds best to direct, clear communication. It's part of why she gets along with Simon so well - he's equally blunt.
At any rate, Micah breaking up with Penny made her change her own behaviors. It's been a hot minute since I read Any Way the Wind Blows, but I seem to remember Penny checking in with Simon more than a few times while they were physically separated. It's also important to note that Penny isn't immediately rushing into Simon's business while she's working with Shepard on his own mystery. She's concerned about her best friend, but she respects the fact that they're each doing their own thing and need the space from each other.
I don't have some grand sweeping conclusion to this, only that I think the breakup was an excellent choice to develop Penny, who otherwise might have remained a fairly static character. She was well-established in Carry On, but she has become well-developed.