My opinions on the advantages of stockingfoot waders + wading boots:
1. Longevity. Both wading boots and waders wear out. Honestly, the timeline has been about the same for me. However, it does separate the issues, so that if one wears out, you don't replace both. Plus, for drying, separation is good. Open up the boots, even get boot dryers. Turn the waders inside out, etc. Extends the life of both.
2. Better boot. Most bootfoots are pretty poor shoes as far as comfort/support. There are a few that are good, but those generally cost as much or more than as the stockingfoot/wading boot combo anyway.
3. Versatility. I've gotten to the point where I have several wading boots and stockingfoot waders. Choice is a good thing. For boots, I have "mostly rubber", good support, hiking type for the backcountry trips. I have studded felt for the slickest places. I have an old backup pair (another advantage, even when you upgrade, you can keep old boots as backups). For people who do the salt thing, you can have a pair of flats boots too.
For waders, I have breathable chest, breathable hip, and wetwading neoprene angle socks. Lots of people also have neoprene chest waders for cold weather.
So when I go fishing, I can mix and match the boot-wader combo to fit what I'm doing, which IMO is a MAJOR advantage.