Anyone think it'd be possible to make a mod like http://www.youtube.com/watch?v=pKSkBEJ_wrM and integrate it into Skyrim's game engine? If so, what would it take to do it? My guess is an imaginative use of the third person camera mode along with the Skyrim map could be part of it?

Secondly, if it is possible to make such a mod would it be possible to insert your own custom made troops into it?

Surely you realize yourself that anything of the sort is utterly impossible.

Yeah, I wouldn't say that anything is utterly impossible, just utterly improbable

Considering what you want to do, it's far easier to make a mod for Total War Rome II - there's already a Morrowind mod for Medieval Total War - http://www.moddb.com/mods/morrowind-total-war