Fallout 3 has a very solid foundation. Me and Doc have talked to no ends about how it could be fixed. No brotherhood, no Enclave, much much sooner in the timeline, maybe a decade after the bombs, no super mutants.
Fuck, Pitt is strongly on New Vegas levels of quality. Stick everyone involved with that as project leads and you'd have a damn good Fallout 3 that fits perfectly with the old ones.