Edit: Chimer_Warrior,
Yes, that's a good point about Tolkien. Like I said earlier in the thread, I can understand something unusual turning up as a part of a story that gets put to rights. For me it's strange that these are walk on-walk off enemies, like anything else in the game. So on your adventures you may come across one of these in a Dwemer ruin, which was before fighting the bear and after fighting the werewolf.
I don't see it like that. I believe that they will only show up inside or around the Dwemer ruins. We don't know what the ruins will look like in Skyrim, but I am sure they will blend into the environment nicely. Also, if the map is any indication, there are not a LOT of these sites, maybe 3-4 in total.
The other thing is, we don't know how much of a role they are going to play. They could have as much a role in Skyrim as they did in Morrowind, or as you said, they could just be another enemy in just another location in the game. I find that a bit hard to believe, although probably not in the mainquest, I think there will be a significant quest or series of quests related to them. I have faith that they won't feel like they have just been slapped into the environment though.