I personally feel that the problem with Headmasters is that the Japanese tried to make it too 'American' without a proper understanding on how to do it and this caused it to become really odd and nonsensical with hybrid elements that don't go well together.
Masterforce and Victory have characters and stories more in line with Japanese Anime without trying to be 'Sunbow G1' and although to an American audience they may seem odd, the story works much better as it's largely consistent with the Japanese style of animation and story telling and therefore more coherent even if somewhat distanced from 'Marvel style' Transformers.