BMW_4.4i you do bring up a good point. I wasn't thinking about the 2004 4.4i's when i was posting. I would assume now that they have 315 horsepower (and some more torque... the number evades me right now) the difference between the '03 4.6is and the '04 4.4i would be smaller. So, disregard me saying that the 4.4i "doesn't compare at all", if you're talking about a 2004 model.
But the 4.6is is much more sporty. It's normal transmission mode is set to the sport mode of the 4.4i, while its sport mode is an even more aggresive sport mode not available on any other X5 model. It is lacking 1 gear though when compared to the '04 4.4i. Plus, the 4.6is comes fully loaded (no navi though, that's an extra $2000), while the 4.4i can almost reach the price of a 4.6is when stockin up on those options. It pretty much comes down preference, and since
dimit3 is thinking of selling the car in 2-3 years, depreciation would also come into play. I don't know which has a lower depreciation value though, but i'll just guess the 4.6is.