Depending on the level of destruction many possible alternatives but we can be sure a capital would be rebuilt in Paris, if only for honor's sake, especially as De Gaulle would never let such a symbol of France in rubbles.
But what would be rebuilt ? Notre-Dame probably, as well as the Eiffel Tower. The Invalid ? Maybe, due to Napoleon's tomb. Same for the Pantheon and the Arc de Triomphe, due to the symbolic. The Louvre ? Maybe not all of it, a modern construction might come in its place to symbolize the rebirth of the Nation. The Elysée Palace ? It would be replaced by a modern building or would be relocated into a surviving hotel particulier (rich private house). Another choice could be to go the Russian way, total rebuilding of every building of cultural worth as it was before the war (see the imperial palaces near St Petersbourg/Leningrad, or even the german imperial palaces in Potsdam to see what I mean).
Depending on the level of destruction on the housing market, we could see parts of Paris built with modern buildings not keeping on with the traditionnal Hausmanian style, certainly outside of the Grands Boulevards. More areas might be built using Le Corbusier's ideas for mass lodging (thus more catastrophic living conditions and future social catastrophes such as the current banlieues).
Overall the architecture in modern Paris would be more diverse and american-style towers may be built earlier and in greater numbers than what was done in the Défense area, but would still be out of the historical center due to concerns with the caves underneath and/or massive floodings.