Hi!
Your first two cases will be fixed in 7.10, as Applicative finally becomes a superclass of Monad. I haven't really looked at your third case, so I can't comment on that. Your fourth case is something I'd really like to see solved properly (*together* with a better record system), but as you say, it could be solved separately.
Also, I don't see why it would be a misfeature to have Eq as a superclass of Ord, or Functor as a superclass of Applicative.
-Stijn