Maybe it was a budgetary thing? With no "clean" shots to work with, the most they could do is paint over the original animation, and probably end up with thicker beams than the originals.
IIRC, they did enhance the shot of Scotty cutting into a bulkhead in The Naked Time. The Phaser had no visible beam in the original.
With TNG, they had the original 35mm raw footage available to rebuild optical FX shots.