Rachel and Quinn relationship, as a ship, offers an alternative to all this show's official queer relationships, in the sense that we see what happens when the characters ultimately remain closeted. Quinn is clearly a closeted bisexual women (or lesbian) who will never commit to an official relationship (cause it's one thing to have sex twice with a woman and for some of your friends to know about it, but it's another thing to have real official relationships in society with people of the same sex as you, let's be honest), and Rachel is a bisexual girl who isn't aware of it (or actually, given what she said to Kurt in season 1, she might have been aware of it, but since she never knew about Quinn, we know the rest of the story). For me, it's obvious that they represent each other's unfulfilled, mutual love. They were just too scared. Quinn too afraid to accept herself. Rachel was too scared to try for nothing. All the hints and hidden subtext surrounding their relationship are pretty obvious.
And I even think that this relationship must have been considered at some point, given all the subtext. But given the era in which Glee was made, queer representation of a main character was practically impossible for many shows (even Buffy couldn't make Buffy character officially bisexual beyond the subtext). So, for representation, they gave us what they could with the secondary characters, particularly Brittany & Santana and Kurt & Blaine officially, whereas they only gave the subtext to the heroine of their story. Also, even if my favorite ship for Rachel is indeed Quinn, I still like Jesse & Rachel. I think they're underrated. They're a really good romance, in my opinion better than the one between Rachel & Finn. And it makes sense that Rachel doesn't end up single. She was a deep romantic. And so the idea that she ends up alone forever because her first two loves couldn't be with her is too depressing and unrealistic. Jesse was the perfect choice if it wasn't Finn or Quinn.