One of the things I love about my TOS Blu-ray's is the fact that I can choose between the new and original effects. I know the show was cropped to 16:9 for Japanese broadcast and I wish we would have also had that version available here in the States as well.
The way I understand it that was a straight forward crop with no significant reframing. Most blu ray players can do this automatically if you set them up that way. I know they put the new special effects in 16:9 but thats like 2% of each episode so not really much of a difference to what you can do on your own already.