Mostly the fuselage and the build technique. The Bloody Baron build video will be a lot closer to the Bloody Wonder MkIII than the Bloody Wonder V1 or V2 build videos. The Baron and Wonder MkIII share the same fuselage.
In my opinion (biased as it may be) the MkIII will survive longer than the V1 or V2 designs. Flight characteristics are nearly identical. So it really comes down to personal preference. Whatever you decide, just build one of the Bloody Wonders. They are a ton of fun!