Does any one have game crossover stories that star the Mane Six, CMC's and The Princesses? Or do you have ideas that you want to share?

Well, i suggest that you look at an excellent series of stories by Tatsurou.
some of my faves are

You Can't Spell Slaughter Without Laughter
Sons of Damas
Wily's Wittle Wub
Melody of the Future
Another Hatchling
The Sparkle in His Eye
and Dante's Little Apple Surprise.