like where did all these peeps get the same basic idea for thier religion if the world wasnt connected thousands of years ago? like why is there always three main deities in most ancient religions?
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I am going to dust off my Anthropology/Archaeology degree for this one, so please pardon the roughness and simplicity as much of my knowledge is near 10 years old and there is a lot of new research being done as we type.
Oral tradition can explain a lot of simularities between Old World religions. People have lived on the the same continent for 10s of thousands of years. As people sprouted what we define as civilization in the Middle East they developed new stories (and augmented earlier tribal stories) to explain the world and thier place in it. (Check out the stories of Gilgamesh.)
When bands of people spread out across the continent, into Europe and Asia, these stories changed gradually over time, but still kept the same basic theme. Over time, these traveling groups developed their own cultural identities and own civilizations, again using thier oral tradition to define the world around them and thier place in it. Since this is a GalCiv forum

, think of our fledgling Terran colonies with low moral and no access to information from the rest of the empire, they often break off to form thier own cultural identity (Independant League in this case) or join with a more influencial power.
Now keep in mind, as people began to come into contact with one another (again), they traded goods, services oral traditions and other cultural attributes that they each found pleasing. In GalCiv we have Cultural Starbases and Trade with major and minor powers (including those former Terran colonies).
In the end, Jeudism, Islam, Christiniantiy, Hinduism and Budhism (et al.) all have some elements that are similar. Using Occam's Razor, this hypothesis makes the fewest assumptions about unknowns. (ancient astronauts, etc...) This is not to say there are no "Alien Civs" out there, we simply do not know and therefore can not use alien influence as a reasonable explanation at this point.