They are using the same engine, so really it would just take some modifications to the code to ultimately work...perhaps eliminate the startup quest and change the "dad convo" a bit in FO3...not sure...but it doesn't sound impossible
I wonder how much we would have to beg to have this functionality pre-installed (might even move a few sales from fallout 3 for people whom never bought it but want to check it out).
Anyhow, good idea? Easy enough to do by just some mods or is this where the developers have to get involved?