East meets West in allegory... and it hits. Christianity has the unfortunate history of being interpreted a countless amount of ways. This can be a good thing, inspiring one's own "personal" search for peace in this world. The problem arises however, when perceiving Christ himself. He is, by many a perception, a perfect being. He is god as man. This is to be an ideal for man to strive. This is an ideal we always fail to meet.
Eastern culture tends more towards balance. Yin and Yang is an example of the equality that exists "within every man." Both dark and light mix it up. Life happens somewhere in-between.
Our protagonist is Vash, a Christ figure for most of the series. However, we soon learn that for all of Vash's light, there is a dark force conspiring against him. This is where the show really shines. Because this is animated fare, we can accept the oft used, "evil twin brother" device. It truly works here. Knives is the perfect yang to Vash's yin... and what we learn is, neither can exist without the other.
Western culture may believe in the ideal, but eastern philosophy accounts for man's true nature. We are all both Vash AND Knives. (See Vash's struggle in the last three eps. before the final confrontation.) And when Vash strolls into the desert with Wolfwood's HUGE crucifix on his back, we know the imagery is overt. But, we accept it because the animation medium allows us to.
It is, quite simply... beautiful.