I honestly don't think they'd have gone with a daughter, because if they are planning on future sequels with a new replacement(or should I say a younger sidekick), a daughter wouldn't be the same box office draw as a son! I'm not trying to be sexist, just honest, because bad ass female roles rarely draw in the crowds that males do. Just look at the success of the Lara Croft films, or Elektra, Catwoman, Aeon flux, Resident Evil,and Ultraviolet. Of course there are exceptions, but they tend to be either cult favorites like Kill Bill where people turned out because it was Tarantino's 4th film, or mainstream sci-fi horror where the draw wasn't the female lead but the creature ie. Alien!
As much as a daughter might have been interesting to see, the future of the franchise seems to be hinged on Indy and Marion's child, and Shia was an extremely smart casting choice for this! He already has a huge following, and is on his way to being one of the Hollywood's most bankable movie stars.