Compareing vanilla's, I liked FO3 better(despite its bad story). After the DLCs for NV, it blew 3 out of the water. I have never played any thing with a story arc/moral lessons like that, and it made NV one of the bast games I have ever played. I hope skyrim's dlc's are as amazing, but with bethesdas writers... well... fingers crossed is all we can do.
Something that might help is if Bethesda plans ahead.
Josh Sawyer cited knowing how many DLCs they were licensed for as being a huge advantage in their design. From the get-go, Bethesda promised them four DLCs, so they knew they'd have four no matter what, and that way, were able to plan for it, tie them all together, allow for NPCs to acknowledge content back and forth between the DLCs and the Mojave (Veronica, ED-E) etc etc.