Who We Become is an ongoing story several years in the making, so some question about what stories to read first is to be expected. I recommend reading the stories in the order listed at the bottom of this post, but there are a few things to keep in mind:

*The human and pony storylines could be read independently, although the two worlds do affect each other.
*Main stories in the same world will be sequel tagged for easy chronological reading, but one world will only sequel tag the other if the connection is particularly significant. For example, Looking Glass takes place before Inner Strength, but Inner Strength is not tagged as a sequel because they're about entirely separate characters in separate worlds.
*To further simplify things for readers, the author’s notes at the end of every fic will link to the next chronological story as well as its sequel. So the author’s note for Looking Glass links to both Inner Strength (next chronological story, despite being in another universe) as well as Playing House (Looking Glass’s sequel taking place in the same universe). This probably sounds more complicated than it is; basically the author’s notes will always point you where to go to minimize confussion.
*There's a fair amount of side stories, which are optional. These will also be linked in author’s notes when it would be appropriate to read them.

Recommended starting point:
Depending on preference, either Looking Glass, Inner Strength, or By Blood or Choice.
Looking Glass is the earliest chronological story, and it is a main story in the series. It's where I would honestly recommend starting unless you don’t care for Equestria Girls or are only here for the romance stories.
Inner Strength was the first story written, so obviously it can be understood easily without reading Looking Glass. It also won't spoil Looking Glass, since they're about entirely different characters. The main pro of reading this first are that it's closer in tone to the rest of the series (romantic drama as opposed to psychological drama). Also, if you're not into Equestria Girls, this is all ponies.
By Blood or Choice predates Inner Strength by a number of years, making it also a good starting point. It's way shorter, so if you want a faster read to decide if the series seems like something you'll enjoy, this is the place to go. That said, as this is a side story, it's an optional read.

The full chronological order. Simplest thing to do is just read down the list (numbers denote main story important to the plot, while asterisks are for side stories):
1. Looking Glass
* Breaking the Ice
* Under Her Spell
* By Blood or Choice
2. Inner Strength
3. Playing House
4. Finding Home
* Up in the Air
* Empty Sky
5. Thicker Than Water
* In Her Shadow
6. In Pieces
7. Piece by Piece
* The Open Road
* The Setting Sun
8. Acts of Love
* Coda
* The Opening Act
* Secondhand Laughter
* A Solid Foundation
9. Just a Pony (Currently writing)
* Miracles (Will write after finishing Just a Pony)
10. Life in Equestria (half done, but then I decided to write Just a Pony first))
* Coloring Outside the Lines
* Untitled Cadance story (coming eventually)
10. Untitled story about the plot twist at the end of Thicker Than Water
11. Life in Everton (coming eventually)
12. Family of Strays (coming eventually)
13. The goddamn changeling story yes that's still happening
(The rest to be determined)