I think the question really being asked is which ski provides the enthusiast with the best balance of both worlds; with the ideal blend of stability, reliability, storage and limited fuel consumption while altogether being still fun to ride and not a complete and total dog on the water?
Although Brian lists all of the best characteristics, there's a couple problems with the Yamaha SUV 1200, namely the two-stroke plant. Unfortunately, two-strokes leave that tell-tale "snail trail" of an oil slick in its wake. While many don't care, the environmentalists who seem to have the biggest sway with hungry-pocketed politicians do care. It's all but impossible to ride a two-stroke PWC anywhere in California that isn't the ocean and - if I'm not mistaken - the same goes for New York, Massachusetts, and New Jersey with several more states in tow.
The Yamaha SUV 1200 is also a toad. Much like your parents Ford LTD station wagon that they piled you in to go to Sunday church services, the Yamaha sacrifices fun for utility. Storage, yes, can't be beat, but at the cost of not being all that fun to ride when the fish just aren't biting. Of course, I make this point when Brian's ski is so obviously 100-percent committed to fishing and - from the looks of it - not much else.

2008 Yamaha VX Cruiser
All the units mentioned here are good candidates. The Yamaha VX and FX units (sans the 1.8-liter SHO series) are great economical and pretty-damned-near-bulletproof skis. Storage is decent and the boarding platform is broader than most in their classes...except the platforms are slightly convex, which may interfere with securing a rack properly. Oh yeah, and Yamaha still insists on mounting its reverse levers directly beneath the throttle on the right hand side.

2007 Sea-Doo GTX Limited
Sea-Doo's previous GTI, GTX and RXT series (pre-2010) are all lightweight, reliable units, even the *gasp* supercharged versions. But the aforementioned complaints are justified, fuel consumption verses that of a naturally-aspirated ski is drastic. Sea-Doo's offer a class-leading water-resistant removable front storage bin that can be fully watertight with the addition of a factory-available lockable lid. This is almost a must because of its convenience.
Sea-Doo's rear platform is perfectly flat and nearly as level, making rack securing a breeze. GTis are the smaller, more nimble units and are best for lakes and rivers while a larger three-seater GTX or RXT would characteristically be more stable and smoother a ride.
Kawasaki's STX series, either the smaller two-stroke 12F or the four-stroke 15F, are both good, hard-working units; save that the two-stroke runs into the same problems with Brian's suggested SUV. STXs are comfortable, simple units that carry plenty of fuel and consume every last drop if you're heavy on the throttle. Front storage can get wet like the Yamahas, but at least the reverse is on the left hand side for better docking maneuverability.

2008 Kawasaki Ultra LX
Kawi's larger Ultra LX, Ultra 260X and Ultra 260LX are are more enjoyable rides, exceptionally comfortable in both smooth and rough, feature removable front storage bins with even more storage beneath, massive fuel tanks and other amenities missing most notably on the Honda-brand PWC. But be warned: the supercharged 260X and 260LX
devours fuel, especially if you're a hot dogger.
Honda's skis are what you'd expect from Honda: not the fastest, not the most dashing, but definitely some of the most reliable when properly maintained and left the hell alone. Hondas typically don't take well to aftermarket performance products. The smaller F-12s and turbo-enhanced F12Xs are a rough water nightmare but are fun and "playful" on smooth.

2009 Honda F-15X
The larger F-15 and turbo'ed F-15X is a far more attractive unit and is - bar-none - one of the single-most stable skis on the water today (also with a removable front bin). Honda, though, is pretty proud of its larger F-15 series, pricing way out of logic's reach. Best go to a dealership and purchase a heavily discounted '07 F-12 for half the price of a current model; most dealers are still sitting on several brand-new "overstock" units.
Frankly, I'd lean more towards "fun" than pure, dedicated "functionality." After all, there will be a point when I'm not hauling my rods and tackle out with me and I'm going to want to have a good time with my ski, and the only time I had a good time doing donuts in my parents' old stationwagon was when I didn't know there was anything cooler or faster out there.