StormShade, I'm so used to TOS as The Original Series on this website I had to re-read your post.
On to the actual subject of my post.
I've always enjoyed the allegorical nature of Star Trek and certainly look forward to these types of missions in the foundry. The one request I have is for everyone to try not to spell out what you are trying to say, just allude to it. When Picard directly linked the forcible relocation of a group of people in Insurrection to what the US did to the American Indians, it's like explaining a punchline for a joke (I am not comparing the treatment of Native Americans to a joke) which makes the joke less humorous. Like it was mentioned before in this thread, subtly is important and makes your story much more compelling.
Which is funny because in the TV series he was going to forcibly remove some native Indians from a planet they had settled on orders from Starfleet Command. Funny that he chewed Crusher out for his own little "insurrection" and then they had him do the same thing himself in a movie. . .one reason why I hate the TNG movies.
Star Trek at it's core was always bringing current social norms into question, but Gene and the writers had a unique way of handling it, and its key to breaching certain topics.
1. Ensure you develop player empathy with the key characters, announcing right off the bat that this Prince is gay, will cause all sorts of player bias' right from the get go. It's important to draw the players in so they see this Prince as "good for the community, good for his people" and that, even though he may not follow the social norms of his planet, his personal characteristics supercede his personal preference for love. However, don't overplay how "good" this Prince is, else player's will want to vomit if it's Prince Awesomesauce.
2. Remember that unlike the TV series, where there is a set script and the actors HAVE to follow it, player's are NOT viewers. Yes, they are taking part in your story, but unlike Kirk or Picard who had to "sell" a certain perspective because the script said so, you are dealing with player's own characters, who have their own preconceptions. It is not your place to "dictate" your version of Utopia and make them follow it. That is the ultimate goal, not to get people to necessarily agree with a point of view, but to see it from a new light, to understand it, and see where the "other side" is coming from.
3. The story doesn't always have to be a happily ever after, or a forbidden love ending. Alot of Star Trek episodes didn't end in Black and White. The ending could quite possibly be that the society just isn't ready to accept the Prince's point of view, and the prince isn't willing to follow the social norm. Maybe the Prince says bugger it, takes off with his love and its the first time the planet is left without a King, all because of their Bias both parties are left worse off.
Sometimes it's enough for a story to draw out different perspectives and points, and cause the player to question, to look inside and see if they too are pigeonholed in set values. This was always a key factor in Trek writing, alot of the episodes were a mirror of current society, to cause people to ask questions of themselves like "am I the racist..sexist etc."
Ultimately if a Foundry Mission like this gets accepted, or gets you banned lies with you the story writer/creator. Are you setting out to tell a story and provide a perspective, or are you setting out to inflame the player base and rock the boat? Presentation of the theme is key.