This is a really good story. However, it's starting to sound like Harry would have been with Hermione if the both of them had been honest with their feelings and now that he and Luna have been together he'll stay with her no matter what happens out of loyalty. There's been very little to show that Harry has real romantic feelings for Luna aside from the normal teenage hormones.
Luna is one of my favorite characters and I'd love to see Harry's feelings for her explored more.
You've basically hit upon Luna's concern, and the reason why she wants Harry and Hermione to explore their possible relationship.
She is wise enough to know that it's all too easy for a girl to lay a claim on an unattached 15yo boy, simply by paying him the kind of attention that she has been. But she wants to be sure her feelings are returned honestly, and she hasn't just won Harry because she's the only one to actually pursue him.
The fact is there has been far more history between Harry & Hermione, and you're right, they should have been together earlier if they'd had a clue.
But don't worry too much about Luna. There have been a number of clues that Harry does have some depth to his feelings towards her.