I haven't received my car yet, so can't say much about the interior ergonomics. As of the things i would change, i agree with some of the things already mentioned:
1. Electric steering wheel adjustment
2. LED brake light and turn signals (incl front turn signals)
3. Better interior quality, in here X3 20d is significantly more expensive than 520d (maybe its our import duties of 4x4 vehicles are higher, or could be because bmw indonesia take more profit for the x series sold here i don't know), if i don't need the ground clearance i would have gone with the 520d just because i feel the overall interior quality is better.
4. Headlight design is too squarish (i'm sure it is mentioned before), and imo doesn't flow with other bmw headlight design, i wonder why bmw always has to make the x3 different than the siblings in terms of design fluidity. Even the x1 has better shaped headlight. That said, no way i'm replacing my x3 with the x1
5. Ventilated seats would be nice, although i'm sure the feature won't make it here, and maybe bmw doesn't want to canibalize x5 sales.
6. Covered cup holders
7. Not too important, but would be nice to have interior ambient lighting a la 5 and 7 series (the lighting strip underneath the door trim)