Four weather features which would be interesting to see in a sim, although probably a bitch to code.
1) Icing. Based on air temp, humidity, local precipitation, etc. The physics of it might be easier to figure out than the graphics for icing on wings, prop, carb, etc.
2) Accurate precipitation. Both in terms of type and volume. Fly into a thunderhead and have your plane get beaten up by melon-sized hailstones. Gain altitude and suddenly the rain you're flying through turns into freezing rain or snow.
3) Cloud and front turbulence. Fly into an 30 km tall anvil cloud and get your plane flipped over and torn apart by updrafts. Fly along the point where two fronts collide and experience clear air turbulence.
4) Wind interaction with terrain. Updrafts and downdrafts near mountains, terrain which blocks crosswinds on landing or take-off, daily onshore and offshore breezes in coastal areas. This would allow realistic air effects when flying through/over mountains or along coasts. Recreate Steve Fosset's last flight over the Sierra Nevadas, supply flights over "The Hump," or Alaskan bush pilot flights.