I've done three onsite stays, all at OKW, and four offsite---three pool home/townhome, and one Bonnet Creek. We only stay in places where the kids and parents have separate sleeping spaces, with full kitchens and in-unit laundry. For us, all of those are pretty important features.
Comparing a 2BR OKW to a 2BR at Bonnet Creek, I like the fact that OKW is a little more peaceful and spread out, but I like the fact that everything at Bonnet Creek is close by---two sides of the same coin. The room sizes are similar---OKW seemed to have a little more space, but BC was better outfitted for a family with more than four (the dining table at OKW only seats four). I liked the large balcony at OKW, but I liked the view overlooking all of Epcot, with the castle in the distance, at Bonnet Creek. I enjoyed the fact that Bonnet Creek had Stacy's Must-Sees on one of their TV channels. My wife hates Stacy, and was hoping to escape her by avoiding OKW.
We thought the bedding was a little more comfortable, with nicer linens, at Bonnet Creek.
Overall, I thought the two experiences pretty similar. I might pay a *little* more to stay at OKW---mostly because every once in a while, we do like the transportation convenience. I would not pay a lot more.
If the choice were between a 2BR at Bonnet Creek, and "just a hotel room" at any Disney resort, I'd stay at Bonnet Creek, even if the cost was the same---in fact, I'd pay more for it. But, that's because I can't imagine staying in "just a hotel room" with my kids for more than one night, or maybe two.
As a caveat: we always get a rental car, and we drive ourselves almost everywhere (including MK after *two* different 1+ hour bus trips to MK in the afternoons on our last OKW visit). We avoid EMH in hopes of avoiding crowds. So, the two big "Disney perks" aren't a big deal to us, except when we're hoping to have a glass of wine with dinner, or a margarita as we stroll world showcase.