Since I was the one to start this thread, I have managed to implement what I initially wanted as F a :: *->* with F a x::*, and the cost of not having partially applied type synonyms was not much apart from some more equality coercions that I wasn't expecting.
The most relevant tradeoffs are some more extra parameters in type classes (notice the d in fmapF) and having to bind explicit signatures to variables that only occur as a type-index to the type family (notice id::x->x).
class FunctorF x where fmapF :: d -> (a -> b) -> F x a -> F x b
fff :: forall d x. (FunctorF d) => d -> F d x -> F d x
fff a = fmapF a (id::x->x)
Generally, I love type-indexed types.
hugo