To be entirely honest, there's a lot of small things wrong in the game, or things that seem to be missing (dynamic events, complex faction relation and interaction, deeper RPG aspect).
A lot of details feel weird and could have had a bit more attention, like Ivefan listed. Even if you love playing it, like me, it gets to a point where it makes you sad.
Then you get back to having a lot of fun just exploring and try your best to forget about it.To me, it's extremely weird how they took many steps at the right directions while, at the same time, taking steps back in stuff that used to be praised.
There's no denying that, even though (again) I'm having a blast with the game, it feels like I'm playing Fallout with the Fallout RPG component minimized.
If I didn't love the setting, atmosphere, survival stuff and the series so much, I guess I'd be disappointed too. But I had set my expectations very low.
I just hope that for Fallout 5 (if that ever gets made), they seriously take all the lessons learned and apply it. They don't even need to brainstorm new ideas - just put together all the feedback and praise from FO3, NV and FO4, polish the systems, and that's it.
IMHO, it feels like they did like the guys from Egosoft with X:Rebirth - they tried a sort of reboot if you think about it (except Beth didn't reset the universe, and didn't completely fuck up and remove critical parts of their game). If they were just releasing a sequel, it wouldn't feel so weird to those who played FO3.
I'm not entirely sure why they'd do such a thing. Some people are hoping there will be a "New Vegas" equivalent for Fallout 4 by Obsidian, and that could bring better news.
If anyone ever confirms that, please let me know.