What if the half-blood prince used to be Tom Riddle, but isn't anymore?
What if she wrote what we now know as Chamber of Secrets with the plan to have it be called Half-Blood Prince, referring to Tom Riddle, but then changed it to Chamber of Secrets.
But she really liked the title and wanted to use it all along.
Now she has another story with a different half-blood (by the way, muggle born people and people with one-wizard/one-muggle parent are both called "mudblood") person, and she was able to revive the title that she liked several years ago, only now it's talking about a different person?
I don't think the person this title is referring to is Tom Riddle, just because I don't think she would flat out say that it's not Voldemort if it is the person that
used to be Voldemort. I think, since she seems to love dropping hints and making us crazy, she would have found another way to put that so that it would leave the possibility open that it is "kind of" Voldemort.
Not to mention, she got rid of Tom Riddle in a pretty clear-cut way... how would she bring him back without making it seem like a soap-opera (you know... he's dead, he's alive again, he's dead, he's alive again, he's coming back as a memory, his memory is disappeared, he's come back as a human......) starts sounding a little melodramatic after a while.
If she's only trying to revive the title, it could still be someone we don't know yet...
So far, very few people have been introduced that I think would be the half-blood prince.