hmm, in Indiana Jones they: removed all religious references, and removed all signs of Nazism, although it's still the Germans he fights. it still turned out good, they just used the basic plot that he's a part-time teacher who travels the world in search of rare artifacts and has to fight bad dudes who happen to have soldiers. for Watchmen... there would be a lot taken out to put it at least at a PG-13 version.. they'd probably emphasize on the Minutemen and Moloch, and possibly make Veidt a villain as well. so my guess is that the basic plot they would use is that the Watchmen fight crime and such, but who watches the Watchmen?
what's interesting is there is a swastika in a European catalogue in the background of Indy set. :http://www.brickshelf.com/gallery/manxb ... g_wing.jpg
they ~ sort of ~ kept in the religious references with the Ark scene and labelling the sets as such, but your totally right, in the toy line and in the game it was a much fluffier version of the movies, although still totally accurate, nothing was rewritten, scenes were cartooned up more.
the Indy movies were made for kids and adults whereas WM is not geared towards kids. I'd be really disappointed if they watered WM down to make it palatable for marketing, this is an instance where I wouldn't want Lego figures because that would mean it's a softened up version. Lego also really likes concrete good & evil, it's very easy for kids to know who the good/bad guys are in SW and Indy, whereas WM you have these vigilantes, anti heroes, turncoats, and patriotic atomic bombs walking around, it's a lot more grey with who's right and who's wrong.