Meh, not a big fan of Fallout... and i'd much rather Skyrim be influenced by Morrowind, Oblivion and Daggerfall than Fallout 3. Similarities with Fallout 3 should be kept to a minimum and disguised to suit a fantasy setting.
Like I mentioned before, most talk of "influenced by Fallout 3" is talking about the game mechanics, programming tricks, background calculations (like the level scaling system). Not exploding heads, guns, and mutants.
So, there's really no need to "disguise" the stuff for a fantasy setting - it's all in the nuts & bolts.