Intuitive Explanation for why more negative charge on ligand does not imply more splitting effect?
Crystal Field Theory assumes that all of the interactions occuring are purely electrostatic and only concern d-orbitals.  This is clearly not true when dealing with some ligands which create a covalent bond.
Most limitations of CFT all stem from the inability to explain non-electrostatic interactions.  For this reason, it works well when the electrostatic aspect is the dominant factor but it completely fails for some cases such as neutral CO ligands.  While you could easily argue electrostatic forces still exist in this situation, clearly they are not dominant and do not explain any observed behavior while still having an effect.