You didn't see those two praised for story because everyone was comparing only their graphics and irrelevant content with predecessors/successors or the competition.
DX:HR lost GOTY title on most sites because the competition (TW2 and Skyrim) had betterlooking visuals. Oh and btw, TW2 has an awsome story, so buy asap. Skyrim story and substories are unbelievably bad. There is no way I'd ever recommend buying that game for sakes of the story.
FO:NV story and substories awsomeness faded under community praising FO3 for huge caves that are not taken as caves but underground facilities because Bethesda applied another texture(s). But once you dive into FO:NV story, you will never want to hear childish fairytale from FO3. Unless you're one of those who wants to grind on endless respawns in too big areas in a game that has a quest or two appearing every 20 hours. And I bet you're not.
But I didn't mention just those two. I've mentioned Stick of Truth too. Make sure you play it. You won't find a story like that anywhere.
I've also mentioned Mars, grab it. The story is not epic as it's a short game, but it's written so good I said back then I'm buying the sequel most definetly just because I want to see in what direction the story will evolve.
Didn't mention adventures because there are too many with good stories. If you will get yourself an adventure or a few, you don't really need a recommentation as most proper adventures have a good story. HOG adventures have crap or no story at all. Don't buy those, they feel like a phone cow clickers and I can't understand why that facebook idiocy is placed under adventures/puzzles genre.
EA games…
One day EA will have to cut the crap. Simcity is just a start. So you will eventually play those games.
I dunno what happened with their script writers. DA2 and ME3 writing, while not a complete disaster, is highly inferior to stories predecessor games had. Hopefully it'll change.