FO3 was definitely more conducive to "open world" gameplay. I definitely spent more hours of game time just raiding Enclave patrols and posts and spent countless more hours hunting the bullet spongy Albinos, Overlords and Reavers. Although the story sort of went off on it's own tangent, I liked it. The intro actually gave you a "taste" of what it was like being born and raised inside a vault. I liked the spin on how the East Coast faction of the BoS went "Robin Hood"and how the East Coast Enclave outwardly used "American" propaganda as opposed to those in the West Coast which were presented as an advanced, ruthless, secret organization, which you only discover later, towards the end of the story that the Enclave is what became of the American military/government complex after the bombs fell.
With that said, I still think FONV is a superior game. Just in terms of enhancements like the Companion wheel, the gun sights, hardcoe mode, ammo types, weapon mods, etc. I'd have a really difficult time trying to go back to play on the FO3 engine. It was awesome to see what became of the NCR around 40 years after the events of FO2. I'm glad that Obsidian and Bethesda teamed up on this one and I truly hope this collaboration will continue for future installments of Fallout.