Watercraft covers are very important. The purchase of a watercraft cover is the single most important thing you can do for the life and good maintenance of your watercraft, whether it's a seadoo pwc, a pontoon boat, a canoe, a motor boat or a sailboat. All watercraft benefit from having a good quality and properly fitted watercraft cover.
The costs related to each watercraft cover are directly related to the size of the watercraft and to a less extent the cost of the watercraft. It goes without saying that you will likely spend more covering and protecting your 75 horse power ski boat than you will your aluminum fishing boat. However, both boats should have a cover.
Of course water craft that have motors or cushioned seating require the most protection from the elements. Sometimes it makes sense to have two covers for your watercraft. For example, I have a lighter weight cover for my seadoo pwc that I use from day to day in the summer months. This seadoo cover is meant to keep the sun off of my paint job especially when I have specific detailing done. I have another heavy seadoo pwc cover that I use when I store my machine for the winter months outside. I also use this heavier cover every time I travel. The heavy cover is a more secure fit so it is safer for taking on the highway. I would never use the lighter cover for traveling as it is looser and would get caught by the wind. It also is less secure and I would worry that it would thrash around a bit causes wear and tear to the cover and perhaps dings to my machine.
For some smaller water craft like kayaks or canoes you would only need a cover when it is not being used for extended periods of time, or in the winter, or if you live in a rainy climate and need to take steps to keep the seats dry.
A good quality watercraft cover should last 50% of the life of the watercraft. This is just a rough rule of thumb. However, you should know that covers don't last forever and need to be replaced from time to time.
Previously only larger watercraft had customization on their covers. These days every one is getting into the game. People are having their names included in the customization of the cover. Competitive pwc racers often have the teams names embroidered on to the cover. Others prefer not to have a name included but rather have another symbol like a tiger or dolphin or some other type of symbol. Whatever your taste a good quality watercraft cover is a good investment.