If I could get this feature in to the game I would create a nemesis that was a Cardassian Gul engineer. Part of the True Way. With human mirror universe officer as his crew, flying a federation cruiser. Bent on capturing me, retrieve my memories, give them to my mirror universe counterpart and replace me with him.
Yes, a Mirror Universe nemesis would be one way to go. Someone like Gul Dukat, Sela, Weyoun, Duras Sisters are other versions
MU would be easy and seamless but I think it would be nice to be able to create the nemesis. Also, it would make sense and save the developer headaches to have it be a random occurrence while patrolling clusters in between the mandatory three or counting as one of the three.
Hopefully, the UGC tool-set should allow us to not only create and define a Nemesis, but also create the missions that Nemesis would engage us in. I suppose if you wanted, you could describe your Nemesis to an in-game friend and they could write your Nemesis for you, complete with story-based missions!