...maybe it's just me, but I always preferred the clouds in FS 2002.
Much more realistic I reckoned, even if they were "only" 2D... ;)... ;D...!
...and didn't affect the frame rates...!
The 3D cloud types, density, altitude, variation, etc, have to be very carefully selected in FS 2004 to make them appear natural... ;)...!
I set my clouds up in the flight sim after taking a peek at the sky and the clouds outside of my house, and compare them... 8)...!
To get good frame rates, I generally ignore complex cloud arrangements and select simple Cirrus or Stratus clouds, and set the visibility to 10-20 miles Max.
This gives the fastest frame rates and avoids processing and showing scenery in the far distance, (which is un-realistic!)... ;)... 8)...!
Remember that the clouds are one of the biggest frame-rate hoggers in the flight sim...!!
Using this type of Weather selection, I get consistant smooth Frame Rates of 30FPS+.... ;D...!
For an excellent, simple, free-bee, add-on, weather program, have a peek here...>>>
http://www.avsim.com/Search for "Weather Maker. Personal Edition".
...and download it...enjoy...!
Cheers all...

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Paul The Weather Man....

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...!
Win 8.1 64-bit. DX11. Advent Tower. Intel i7-3770 3.9 GHz 8-core. 8 GB System RAM. AMD Radeon HD 7700 1GB RAM. DVD ROM. 2 Terra Byte SATA Hard Drive. Philips 17" LCD Monitor. Saitek Cyborg X Fly-5 Joystick. ...and a Briggs and Stratton Petrol Lawn Mower.