I'm in for simplified weather, too. Don't need to get realistic (high/low pressure zones, moisture, etc.), just wind that comes and goes, rain that comes and goes and some aesthetic clouds are enough for me.
I would not like seasons that don't make sense. If there is no tilt and no noticeable eccentricity, I'd rather have the climate stable and just go for short-term variations.
The way I see it, winds would add to air speed when calculating aerodynamics; rain would be a drag-type force. As for which way the wind blows, I'd simply throw in a couple circular streams plus a bit of this (or a less computer-intensive version of that), varying with temperature/pressure (which in stock already vary based on latitude/altitude/time of day).
Second thought, that method in the article I linked doesn't seem to be too intensive, considering you just need to calculate a single vector on the field at each frame (for the ship's center of gravity).