It seems like we're expected to not ship Donna and the Doctor because they are individually complex and interesting characters.
Throughout their time together, their interactions are built upon giving deeper insight on who they both are individually, rather than extensive shipping fodder or teasing about the nature of their relationship.
Donna doesn't save the Doctor at the end of The Runaway Bride because she was the only person in the world who could have. She saves him because that's who she is. She is kind, and compassionate, and empathetic, and there's no way she would have left him there.
It's not so much a grand commentary on the nature of their relationship, and how they are 'just so cosmically meant to be', as it is a moment for her to show us (the audience) who she is.
It's not because he already has some kind of undying love for her, he never would have listened to anyone else, or because he's willing to live only for her, or any of that.
It's that she's the kind of person who reaches out and cares even after a really rough day, when the spaceman is scaring her by drowning spider babies.
The moment is about who she is.
And they keep being allowed to be like this, where their interactions aren't relegated to being only about their relationship with each other. If anything the way they interact with each other is used like a launching point to deepen our connection to each character individually.
(Probably because we're not supposed to ship them lol. Okay definitely.)
I have to come back and elaborate on this with further specific Doctor/Donna when I get the braincell back from Bora Bora, but basically:
I love a fictional relationship where the writing is focused on deepening my understanding of and affection for each character individually, and then letting me come to the conclusion, based on an intimate understanding of each character's deepest convictions, insecurities, fears, and values that I want these two to be together.
The thing is, there is a wealth of writing out there that spends all of the character's screen time telling you to ship the characters, all too often at the expense of our investment in the characters as whole people outside of that relationship.
In my tastes, it is far more compelling and satisfying have the chance to fall in love with both characters individually without the writer feeling the need to bathe every moment of interaction in big flashing signs telling me: THEYRE EVERYTHING TO EACH OTHER!!! GET IT? LITERALLY NOTHING ELSE MATTERS!!!
It's so literary to me. Pride and Prejudice isn't iconic because Lizzy and Darcy spend every moment together, talking about each other, pontificating on the nature of their relationship and why a hypothetical reader should totally ship them.
They actually don't have a lot screen time (or page time) together.
It's iconic because we get to see who both characters are, what they value, how their failures affect them, why we should love them both.
And for the majority of readers, loving them both is enough to convince us to love them together. Why? Because we know them well enough to know they will be good together.
