Indeed, the redone visual effects and clean up that Lucas had done for the original trilogy kind of makes them seem better than they are. They were top notch for their time as was ST:TMP except that it was done on a VERY tight schedule with little time to go back and do the clean up that one...
As others have noted, the visual effects were pulled together on a tight schedule. Some issues with matte lines aside, I think Trumbull and Dykstra did a fine job with the visual effects.