The alien theme can work I think in Indy, but they didn't go right about it, it was a bit too obvious with the alien exposed and the saucer. In fate of atlantis, the indiana game, there are alien references and so forth. At the end, the Germans attempt to make themselves like gods and they become strange scary looking beings of light, which eventually become deformed and die as a result. We don't see any aliens, but we see deformed bones and hints maybe the technology was from above.
I don't mind the ending with the alien in KOTCS, but, they should have made the death of Spalko a little more harrowing. I thought the alien when it leaned forward has quite a cold scary look in its eyes, actually. I think the scene where the bodys slide together does look good to be honest.
They could have had the alien figure somewhat darkened in shadow and not expose the full mystery of its apperance.
But, I think what would have been best would be like the comic. Irina's eyes should have burned out but she is still having knowledge poured in to her so she is still "seeing", whislt this occurs the skeletons (even if from camera trickery) appear to be closing in on her, until the beams set her on fire from the inside out. In this case, we'd never see the actual aliens but simply a sample of the power.
OR they could have made it so when she alien appears before her, it is clear she is seeing the skeletons as they would have appeared in the past in their full form, since she is being given the overpowering knowledge.