Actually, I found the stories and characters to be one of its strongest points. Except the main quest that is. Strictly speaking about the main quest, I would have to say that story was short, linear, and uninspired. The ending was very anti-climatic. I think I would have fonder memories of the game had I turned it off before ever witnessing the ending; at least then I could speculate. :/
However, the rest of the game had plenty of quests and characters that were interesting and original. Many of the characters' personalities were unique enough and developed enough that I feel like I can easily imagine how each one of them would handle a particular situation and why. That's a LOT more than I can say for most games' NPCs with maybe the exception of 1 or 2 of the main characters. The quests were also a breath of fresh air since there were about as interesting and varied as I could expect.
Exploration was also quite cool. I was never more interested in what was in that structure just over the next hill. Some of those locations, especially that one place which left a purple taste in my mouth (I call it that for spoiler reasons), were almost as creepy and "edge of the seat" attention-grabbing as a good suspense movie. I say Bravo!
The only problem (aside fromt he main quest and ending) was that exploration lacked in the "loot" area. There was very little equipment to find. There were a few weapons for each weapon skill and a somewhat unique named version of each but that was about it. There were a lot of lateral additions to your arsenal but few upgrades. And most of the upgrades that were there came from quests, not exploration. Maybe if the craftable weapons were more useful and the extra schematics brought better improvements it might have been better. Also, they should have put in schematics for weapon and armor upgrades (More armor, lighter weight, less recoil, etc.)
Mods helped me out a great deal though. I found one mod that SERIOUSLY reduced the amount of supplies you get from and during quests. That really made me raid the ruins to stock up on supplies for a mission.
Edit: Oh, and one more major problem; the quests need to have bigger impacts based on how you complete them. I applaud the varying ways in which you can complete a quest. I applaud the way in which the reward and quest dialogue will change based on those actions. But what the game needs is post-quest effects. If you complete a quest by killing Jimbo, then that should open some doors for you while closing others. Perhaps if you kill Jimbo you will get a bigger reward, but if you keep him alive, you can perform quests for HIM and go down a different path. That would seriously add to the games replayability and would really make you think harder about what you do.