Fallout 3 did have some features, the radio, megaton and few others where the players actions did impact on the game world(though only through a polarity and without real impact on the ending, I laso felt F:NV had a bit less of this), but just take some of the lessons from there (it has been 4 years now, time enough to analyse and learn from it) and build on this instead of trying to reinvent the same wheel. Skyrim was good as a sandbox, but in terms of narrative design it did feel a step backwards.
One of the barriers for emergent narratives before was asset storage, and this is not longer such as big issue (with the 10+ GB games becoming a standard...), I do see it now becoming more and more of a design issue then a practical issue, but it is also easy to get stuck in the old ways ("It will not work, we have always done it like this"), which is just as much part human nature as innovation.
Will require more work? most possibly. Will it result in shorter games? maybe, but I wondering if I would not enjoy more a truly emergent game of 20+ then a linear games of 100+, emergent narrative also do have more replay value. The extra work may have impact on price, but I feel the price of games lately have been decreasing anyway, so there might be a balance.
Artistically, there may be another issue, just imagine spending days creating assets for a branch which then no player discovers or chooses... which is why gamedesigners spend more time on "good" choices then "bad", as player tends to go for this when playing properly (they tend to go for "bad" for a laugh or curiosity)
anyway, wall of text...