Make being a dialogue character more interesting than "See this option here? Click here for the diplomatic route!" Fallout 1 and 2 made the whole dialogue option an interesting and complex puzzle that opened funny and in character dialogue that was why I liked playing the diplomatic character. Getting rid of that made the whole diplomat aspect seem shoehorned in.
Make characters unique unto themselves. Okay, was kinda cute that they made Liam Neeson's character look like you, but, when you play an African American female character in a desperate attempt to get away from RPG's usual "white as the snow, brown haired male" hero, and see someone looking akin to Morgan Freeman talking with Liam Neeson's voice, it seems a bit odd. Now, someone is racist in this, either I'm racist in thinking that it's odd to think an African American having Liam's Black Irish brogue, or, more likely, Bethesda feeling that they can black or brown or yellow face a character and hope not one will notice.
Make consequences less predictable. One thing I loved about the whole Tenpenny Tower mission, was I went and did negotiate with the tower to let the ghouls live there, then left, and a few weeks came back to find the ghouls ate everyone. This tickled me pink, seeing how people had done things outside of my field of view, that they had their own events.
Make both character stats, and skills actually have a play in the game. The stats as a whole seemed to have done very little. Sure, they did some minor things, but outside of Strength (carry weight), Intel (level up points), and endurance (Hit Points and resistances), the SPECIAL system seemed to do very little. As far as skills go, weapon stats seemed to do very little to help or hinder, and it seemed like the Speech stat was broken, even at 78% I was losing events at 25%, and it wasn't until I just cranked it to 100% that things worked.
Over all... just don't call it Fallout. The game over all seemed to be good, but don't paint a Buick Regal blue and call it a Shelby Cobra. The car's fine on its own, but don't raise people's expectations.