I know what you mean, but I'd say it's just a case of shifted priorities. I mean, they don't just take Skyrim and slap some new textures on it to make it Fallout (despite all the Skyrim With Guns arguments that would suggest otherwise). As far as I'm aware they tend to build each game up from scratch and start fresh.
The team probably had a board of things that they wanted to do with the game, and refining the sneak and assassination aspects obviously just got over-stepped by something else. Whereas in Skyrim, assassination and sneaking is one of the 'core' three playstyles (The Warrior, The Mage, The Thief), with multiple entire skill-lines and actual lore based mythology devoted to the art - poisons, illusion spells, Gods of Treachery and Deceit etc etc. So I can kind of see how/why it got more attention and polish.
Can't say I've tried a melee sneak build in Fallout, but yeah I can imagine it to be pretty awkward. Swinging a sword is awkward enough as it is. Every time I see it I just go ... "That's not how this works, that's not how ANY of this works!" *facepalm*