From a financial perspective, Fort Wilderness is generally less expensive for us. We usually have 6-8 people, so we're comparing two hotel rooms to one FW site. Also, it's usually less expensive to drive our motorhome to Disney than it is to buy airline tickets for everyone. That said, for us Fort Wilderness is not about staying at WDW on the cheap. Even if it was MORE expensive, we'd choose to stay at Fort Wilderness. We've stayed at the Value Resorts, we've stayed at the Deluxe Resorts, and we've stayed at the Fort. Fort Wilderness is by far our favorite place to stay on-property. We have our own beds and our own stuff (much more stuff than we bring if we weren't bringing the camper). We can bring our bikes, and our fishing poles, and our toys and games. Our camper has nearly as much space as a hotel room, and it's set up the way we like it. We also have the great outdoors and can spread out over our site. We have the option to bring our own food and not be tied down to eating out for our entire stay (eating out gets old after you've done it a few times, IMO). It's great fun to explore the campground by golf cart or bike, to check out the different setups folks have and to see the wonderful decorations during the various holidays. Also, Trail's End is my kids' favorite restaurant at WDW. Since the first time we stayed at Fort Wilderness (over a dozen trips ago) we have not been back to a Disney hotel.
FWIW, Fort Wilderness has the nicest bathrooms/showers I've ever seen at a campground. It also has wonderful laundry facilities.
We've only stayed in one premium loop, 400. It was well located and quite nice. I'm not sure what the status of the loop conversions is, but we've stayed in 200 and 1400 when they were preferred and 1000 when it was full hookup, and each of those loops was quite nice and had its advantages. 200 is close to the action at the settlement and marina, and 1400 and 1000 were well located near the Meadows pool, trading post and campfire program.