I was going to post a response earlier saying that I didn't think the movie was that hard to understand, though obviously there are multiple layers that reward further scrutiny, but I held off because I decided it was too obvious to mention. Some comments posted since then make me think that I must have been wrong about it being obvious.

I still think the storyline is pretty straight forward. Aliens help early hominids take the next step in development, leave a beacon on the moon to let them know when we've advanced enough to leave the planet, and leave a device in orbit around Jupiter to help us advance to the next level.

I think the key as to whether or not one appreciates this movie is how much effort they're willing to put into thinking about and teasing out the extra meaning in the different layers. If you don't feel that it's worth the effort, you probably won't like it.