I guess if you are used to Star Trek next generation and people acting like adults its harder to wacth Prometheus. Also I hate religion so that left a foul stench in the room for me. It took a lot of stuff from alien as well. i guess if your not christian or were not raised christian youd miss all the jesus inuendo.
I like Star Trek Voyager too cause they use "Q" a lot.
In terms of religion, I can't say that I have a problem with Prometheus making references to it. In fact, I'm somewhat glad it did, as I have not seen any sci-fi franchises address the issue much at all in their respective settings. I've always wondered why fictional depictions of the future never address where religion stands in them, even though over 70% of the world today, believes in one. I guess there's no way to do it without offending people.
Star Trek always has lots of episodes about "religion/spirituality" but they call it superstition a lot of times and they talk about it as pas-tense and primitive as something the world used to believe in but have evolved from.