For some reason, I hate the cheap replacement seadoo covers you can get on eBay, Amazon, etc... A new OEM Seadoo cover is about $250+ and not easy to find.
I live in an area that doesn't get too cold in the winter so the ski is fine left out until ready to ride again (I put STA-BIL in the tank and bring the battery inside hooked up to a bettery trickle). When Spring rolls around, just a quick exterior rinse, put the battery back in and it's ready to ride. No problems. Since I leave the ski out all winter, I leave the cover on all winter. I'd rather the cover take the sun and occasional rain beat down, than the ski.
I cleaned it with a mildew stain remover, then soaked it in a big storage tub filled with hot water, laundry detergent and some bleach cleaner. It didn't come out looking new, but much better than it did. Good enough to continue using.
If anyone has some magic cleaner that works well on boat / jetski covers, please let me know so I can try that next time I give it a thorough cleaning.