Advantages..... the stock shock on any B4 out there was most likely sprung for someone who's 110lbs, and I've never seen a stock shock from a 90's bike that wasn't drastically under dampened. So with a quality aftermarket shock, you get the means to use the Right spring for your weight (related to sag without abusing the preload, and keeping the bike from squatting while coming out of a corner, which means you can keep a nice tight line), and can adjust both the compression and rebound damping through internal (major adjustments) and external (fine tuning) adjustments. This means that you can get the shock to work properly and keep the rear tire on the ground, better able to deliver power, accept braking or cornering stresses. And finally, you're able to set the ride height to get the optimal swingarm angle (which is most likely just shy of 11* when unloaded) for the best handling.
I'm very much not a fan of stock shocks and those swaps because they Can be dangerous and way too many people make the swap without knowing even the basics of what kind of spring rate they're going from and to. They just look for something that Kinda fits, and make it fit. Not all shock linkages (actually, very few) use the same progressive compression ratio, and some don't use linkage at all. So while the shock make feel alright at a standstill, it could get WAY too soft/walloy when compressed, or it may not compress much at all which will lead to piss-poor efficiency (and efficiency is what motorcycling is all about) that can lead to crashing.
But that's also why I said what I did above about ignorance being bliss... I've evperienced the best, know what it Should feel like and just how good that is. I could never go backwards and be happy now, and would most likely never ride anywhere Near as hard for fear of a poorly performing shock. Most riders don't get to really experience the best available, and thus they only know the best that they have experienced and have no idea of just what they're missing.
I get the feeling is also comes down to personality. Some people want to do things right, others want to do things right now.