(TLDR at the bottom, thanks for reading.)
Who are you?
How do you define 'you'?
Does anyone truly know who you are?
Bloom into you is a story about identity, and not about what you think your identity is but how people around you think of you. There is a concept in sociology called the looking glass self, the looking glass self describes how people base their own identity on how they believe others view them, this is essentially the core of bloom into you.
There is a surprisingly meta part of bloom into you where the characters have to make a play, and this play focuses on an amnesiac who has lost all sense of self due to having no memories. This amnesiac is then visited by a friend, a family member, and a lover. These three people both tell the girl who they think she is, but she ends up getting three completely different answers. Without an idea of who she is she ends up choosing the lovers answer and starts to pretend to be what she thinks she is. This makes the main theme of identity very apparent to the viewer but more importantly, it presents these ideas directly to the characters.
The main character arc of Touko is her coming to a realisation of who she is and accepting this fact. Touko hates who she thinks she is, the idea of herself she has is far away from what she thinks is good, because of this she attempts to bury this. She attempts to bury this by wearing a mask of what she wants to be, her sister, as she idolises who her sister is but when she talks to Tomoyuki she ends up finding out that her sister was also wearing a mask and that she doesn't really know who her sister is. But if the person she was modelling herself after doesn't exist what does she have? This shows the real reason why Touko was wearing her mask because she was lonely, she states that she "I can not get back to the empty self she was before" but with no mask, she has no one to copy. That is until she finds Yuu, Yuu is someone who sees's through this facade and Touko feels that instead of trying to be her sister she can just live as Yuu see her, becoming the truest version of herself, she blooms into herself.
And then there is Yuu, Yuu is an odd character because the story doesn't really focus on her, despite her being the main character of the story. Yuu's character is really shown as she is used as a tool to show Touko's true self and not her projected self. Yuu is present as a character that is detached from love, after consuming so much shoujo manga and music she has this idea of what love is and because nothing she feels comes close to this. And because of this detachment from love, she feels alienated from peers and feels lonely and isolated because of this. But then she meets Touko, who manages to fill this hole in her just as she helps fill the hole in Touko. They both bloom into themselves through each other.
Maybe Touko loves Yuu because Yuu is the only person who knows Touko.
However, I do have a few issues with this anime. There are times when the show feels like it is trying to pander to a crowd of yuri fans. Does it make sense that Touko wants to keep kissing Yuu? A bit. Does it still make these scenes feel out of pace? Yes. There are also a few characters that had a bit too much screen time for what their role in the story is. I understand that Sayaka's purpose is to cause Touko and Yuu's relationship is too develop but for what she brings to the table she gets too much focus. These elements are added in an attempt to make the story more enjoyable and while they do sometimes achieve this it just seems like they are occasionally haphazardly used. And also the lack of a conclusion (in the anime at least) can dampen the overall experience.
But even with these issue bloom into you manages to stand head and shoulders above other shoujo-ai anime by not just being another romance story, and not playing to the same tropes and themes as its contemporaries and carving its own identity, and that's what makes it special.
TLDR: Bloom into you is as much a story about love as it is a story about personal identity.