If this was implemented, I'd want a change to how 1/7 water covers objects, or the rate at which it evaporates, or the ability for dwarves to clean it. My current map STILL has large, totally featureless areas where I had to drain my perpetual motion machine some odd years ago, not to mention the roof of one building which has been made indistinguishable by an unfortunate pumping accident. I might abandon a fortress out of pure disgust if I had to look at a map that was completely covered in water all year round because the puddles wouldn't evaporate before another storm.
And I'm pretty sure it would solidify any lava that was open to the air... Which would create interesting results. I imagine there would be lots of disasters where a block of obsidian formed without support in a large magma channel, causing a collapse that punched through every level of a fortress, flooding it with magma.
While this would be fun, there would be far more occurrences of a magma feature simply getting clogged up by the stone, requiring it to be dug out again, which would be a pain. Magma moats would be effectively useless, and magma pipes would slowly form an obsidian cap, after being cleared of imps by tons upon tons of obsidian collapsing inward when the water didn't land at the edges. Not to mention the constant collapse alert spam.
Though to be fair, this would lead to some interesting technical details when it comes to magma features, such as roofs to protect against falling rain, and channels to direct flowing water away from them. It would also limit what could be done with magma however.
Also, this would effectively irrigate every tile on the map in a single storm... Which is hardly realistic. That would need to be changed as well, or muddied stone tiles would have to be changed to only support a certain number of crops before they had to be irrigated again.
All these things considered, I'd rather we just had seasonal floods that originated from rivers. The storms can happen offscreen. Or you could have the floods correspond with the storms we already have onscreen. I believe I remember hearing somewhere of a megaproject that could create a similar effect to what you're suggesting, however. Something about building a huge cistern in the sky with a bunch of randomly opening floor hatches.