Yamaha and Seadoo are pretty much 1A and 1B. These two companies together control over 70% of the PWC market.
You already stated the main difference. Yamaha is water cooled and Seadoo is liquid cooled. No different than an outboard motor, the Yamaha should be flushed with a water hose if used in salt water. However, even the Seadoo should be flushed sometimes as well; although saltwater doesn't go through the motor, it still goes through it's jet system. Which one is a better system? Beats me. At the end of the day, I think they are about the same. While Yamaha may need an engine flush, Seadoo will need extra maintenance on the cooling system.
Both are about the same price range. Price is primarily a factor of motor and options. The cheapest PWC's will have the least HP and will pretty much be stripped down on options. The higher end models will have supercharged motors and a lot more options. Heck, I think Seadoo even makes a PWC that is in the $6K range. It's very much stripped down though. Yamaha's lowest end unit is around $9K.
For either brand, you are looking at $10-12K for a middle of the road model.
Also, you did mention fishing setups. While I do not have one, I do know that since Yamaha is water cooled, they have the water ejection on the back platform of the ski; hence the rooster tail of water you see behind a lot of PWC's. This can somewhat get in the way of some of the fishing setups people have. Being liquid cooled, Seadoos don't have this, so you don't have to worry about building something around the water ejection port. This may not make sense if you aren't familar with PWC's.