I love both, but whereas BioShock is excellent in virtually all those areas (bar the lightweight U-Invent system) Fallout is a lot more rangey.
Fallout's lack of upgrading in weapons is appalling, the handful of DIY weapons aren't enough when the only alternative is finding a unique version of normal weapons, least of all because finding extra blueprints (silly idea anyway) is redundant since you have to max repair.
The repair system is silly - take a few shots and your gun falls to pieces, the hell? Then you have to hope you find more of the same by chance, yet the relevant skill's called repair, not replace. It just doesn't work well.
Settlements are too few and too sparse. The other thing is that both the book and futuristic equipment trade-ins have glaring omissions. The book scribe won't except skill books, despite giving the spiel about even childrens' books being useful. The outcast won't take outcast or brotherhood armour (the hell not?) or gatling lasers. That's just sloppy.