Oooh....I like that idea~

One thing I'd really like to include is the fact that the natives of Atlantis were gifted with longevity. 

1. Your princess could keep a piece of her crystal, or since she is linked with the crystal she still has longevity on her side. After being sent to the surface she learns painfully that she isn't like everyone else (either due to her appearance due to her Atlantean heritage or the fact that she doesn't age normally). This could lead her to holding everyone at arms length throughout the ages but she meets your male and eventually they start a friendship or whatever even though she knows the outcome of such things. This not only gives us a bit more to our story but it brings in your male, who could get mixed up in everything as well.

2. I was thinking that after the deaths of the king and queen and the exile of the young princess, a new king (or queen) was chosen to rule Atlantis (since they'd need some form of a ruler). The new king/queen takes the talented young Atlantean boy as their own child and he becomes somewhat of a prince. His adoptive parent(s) gave him a slave-guard, one of mixed heritage (Atlanean and non-Atlantean) who slowly becomes the closest thing to a sister he has. His guard is chosen to accompany him to the surface in order to find the exiled princess. This is how my female would come in~

Now as far as plot things I think it'd also be kind of interesting if they only wanted the exiled princess for one thing - to bring stability back to the crystal. They know that the ones chosen to the crystal typically never return to the world of the living since they become part of the crystal itself. This does two things for us: gives motivation for not only restoring Atlantis to it's former glory but it also gives the new royal family a way to permanently end the former royal line without really having to do the dirty work. And it gives our characters a bit of conflict. My male and female know what the exiled princess if going to be used for, they just don't know that they are sending the princess to her death. They'd learn about that later since the elders of Atlantis would keep that secret from everyone and only a select few would know their true intentions.

The current royal family is illegitimate and they can't send one of their own to the crystal since that person would be rejected. This gives us a bit of background with Atlantis since the current king/queen would declare that they were the true heirs to the throne but the former king and his wife stole it from them. We've got our bad guy right there...so that's all I got...