I'm not 100% against the whole "Alien" thing because the Crystal Skulls really do exist in real life and it is true that we still don't know where they came from or who built them since there are no tool marks anywhere and people do believe all 13 of them hold information inside of our past and only 8 (I think) have been found.
I think they could of gone further with the story and less with the whole "SpaceShip" idea, maybe add Area 51 and more of the Government trying to gain Control of them From Indy or something.
I mean, if these actuarially exist and the theories of them being from outer space really exist, I think it was Great to put it in an Indy Flick.