We are told right at the start that Breq/Esk is from a society that does not specify gender, that by default she uses "she" to refer to everyone, that she is currently in a society that does consider gender to be important and has trouble figuring out which pronoun to use when speaking their language, and as a result of that society it is made clear almost immediately that she is actually female.
So we know the gender of the main character, and at one point we learn the gender of the secondary character (she uses the wrong pronoun in that other language and is corrected on it) but once the story leaves that first planet you have to guess for everyone else.
This isn't the first book i've read that's been indeterminate about genders, but this is the first one i can recall that has defaulted to "she" for the pronoun. I suspected that would end up bothering a number of people, and a quick check online after finishing the book seems to indicate that's correct.
So i don't know what the author originally intended, but here's what i guess:
#1 It was meant to rub people's noses in their assumptions about gender. Some of the people complaining about the default use of "she" in this book claim to have had no issue with the default use of "he" in other books.
#2 It was meant to show how assumptions about gender influence perceptions. It seems like some people are more distressed by the idea of starting out with the assumption that someone is female and then having to decide if they're actually male than to do the reverse.
#2A Part of that is probably the fact that per #1, people don't question it as much if the default pronoun is "he", using "she" forced people to ask that question of themselves more often. Which just goes to show that "male" is often the default answer, and given the way many SF/F books are written you'd be safe to assume everyone is male by default and the exceptions are female. By using "she" for everyone you're forced to one of two possible conclusions, this book has a lot more female characters than is usual, or you're making the wrong assumption a lot.
#3 And this is where it starts to get a little meta. People have complained about the author not using an actual non-gendered pronoun. "It" and/or "they", or making up a new pronoun, or using one from an existing language that has non-gendered pronouns. However it seems to me that in the language itself the word _is_ entirely gender neutral, it's only being presented as "she" in the English "translation" because we're viewing the thoughts of the protagonist, who is female.
#4 Which kind of wraps around to how our own biases and assumptions influence our views of gender. Breq/Esk mentally interprets the pronoun as being female because she herself is female. It would be very interesting if in one of the sequels we switched to the viewpoint of a male character (and there's an obvious possibility for that) and in that book the pronoun was rendered as "he" all the time. Especially when referring to characters who were in the first book and were previously consistently referred to as "she", or in the case of Breq/Esk that we know are actually female. I think that would be a problematic choice to start the series with, but it would be very interesting as a mid-stream switch.