A lot of Scalaz and Shapeless duplicates things that were implemented less well in the standard library. E.g. standard-library tuples can't be abstracted over (supposedly will be addressed in Don Giovanni but that's at least 3 years away). Standard-library futures aren't completely controlled (and overuse implicits) so there is scalaz-concurrent Future which is almost but not quite the same. The macro implementation is clunky and really needs a couple of minor changes that are going to be in the next release but aren't at the moment, quite possibly because it was implemented by an academic whose time didn't quite sync up with the scala language release cycle.
Slow compilation, many ways of doing things instead of a well-defined Scala-style, inheriting lots of Java libraries and having their perhaps very un-Scala-like behavior littered all around, two communities of programmers (roughly) the Java-alikes and the Haskell-alikes