NOTE: LEGO Indiana Jones 2: The Adventure Continues will be, in a sense, follow LEGO Star Wars: The Complete Saga.
Obviously, they will be adding the "Kingdom of the Crystal Skull" element to the story but things have been said that will change:
There will be a new feature never before seen in a Lego game before; The Level Creator: allowing players to make their own levels and environments for them to play around with.
A new variety of characters will be added to the criteria. Not only for Kingdom of the Crystal Skull but also the original trilogy.
All the levels will be redesigned and tweaked to give the next-generation consoles a new beating.
AND
The game will add new levels to the original trilogy to open the experience of the franchise.