Yes, the stakes are higher in FO3, but what starts off as an interesting story turns real cliche real fast ("you must defend the people of the wastes from the evil Enclavenazis who murdered your father and want to commit genocide!"). It's basically every generic sci-fi action film ever. That isn't to say the main storyline was completely throwaway (I really liked everything pretty much up to the point where the Enclave shows up and is generally evil at your direction), it just felt too constricting and cliche towards the end for my tastes. Would've liked to side with the enclave tho. If I can nuke a small town I want the ability to side with the genocidal amerinazis dammit!
Also I am real salty the Outcasts didn't play a bigger role because holy crap their armor looks cool. I mean just look at this:
For people who prefer tackling more political issues, there is NV.
Now NV wasn't without its share of issues (Caesar's Legion was seriously cartoonishly evil in how they were presented, the locale wasn't one we normaly associate with a post-apocalypse (although they were closer to what the world might look like 200 years after the bombs fell than FO3 ever was)), but it did give a more interesting and nuanced story instead of the "hey the nazis want to use this power for evil" of FO3. You felt like your decisions impact the world on a larger, more complex scale than just simple "defend the people from the nazis", there was a feeling of being either a pawn or a big player in the grand political scheme of things (depending on the main quest line pursued), capable of inflicting a lot more long-term consequences than "the people can now drink water without fear of genocide" (you might think this is immensely relevant, but in the grand scheme of things it just gives the powers that be another reason to fight over). It felt big, but not in that "I am a badass, here's my power armor, here's my gun" kind of way, rather in a more "my choices here might have long-reaching consequences that might not be readily apparent". (although they probably won't have since I'm assuming that Bethesda will do the reasonable thing and pursue their east coast 'verse with their fallout games as it gives them far more creative freedom)
Then again, I probably wouldn't care if FO4 is about you trying to save a forest village of Ewoks from being exterminated by the evil Enclave Lumberjacks as long as there's an interesting world with lots of compelling sidequests and locations to explore and people to meet. Honestly, the only thing I really want is a 50s retrofuturistic open world RPG/FPS hybrid without any of that colour filters nonsense and I'll be happy.