Warning!! Spoilers:
I thought it was pretty good but there was ALOT of things that just didn't make sense. First obvious one being, how is it that you need one of the crystal skulls to get into the room where all 13 aliens skulls are? How did someone take one out if you need a skull to get in in the first place? How did the Russian people get down to where Indie and the other people were if the steps to get down slid into the wall?
Also, I find it annoying that these aliens supposedly came down to teach the Mayans and then leave them in peace, then they explain how the city of gold isn't about gold at all, but its about knowledge and yada yada, so how come the aliens are violent and just kill the bad guys off at the end? Where is this 'knowledge'??? Were the aliens just mad someone took his head, and whoever returned it would just be killed in retribution?
Why couldn't they make the ending leaving you with happiness and joy rather then aliens killing people?