hmm i love to fly in all sorts of weather - it keeps fs fun and varied, but i'm usually stuck to a default setting of mine as rain and thick cloud just kills any smooth flying from the vc, even in 2d it suffers into a 15fps jerk-fest.
i've never messed with weather - though i do have smaller textures for the clouds. what kind of tips and tricks are about to flying in bad weather?
You could try lowering other settings such as ground scenery etc - if you are in thick cloud, then ground scenery isn't paramount. Like you've said, there are quite a few downloads available to change the intensity of clouds on your system which should help a bit.
I rarely fly in thick cloud for that reason, but I'm sure if you tweak your other settings and shut down all programs before you start FS9 to reserve CPU space, then it shouldn't stutter too much.
in "settings > display > weather" settingsyou can change the weather sliders, such as cloud density and draw distance you could play with them to make it more FPS friendly, if you turn them down too much it won't look quite as good though