The episodes are almost unwatchable after seeing them with the crisp new CGI FX, they're close to being totally seamless...
No matter how many times you say this, it still isn't true. The effects were cheap looking and didn't match the live action footage. Do we really need to pull the images of the low-poly D-7 again? Sure we do!
The FX were replaced because the old FX do not stand up to the new HD transfer, and unlike STNG-R, none of the original elements exist to recreate them....even if they were, I would suspect the camera work, lighting, and detail of the time would still not be up to today's standards, therefore the decision to update was pretty easy, if not inevitable.
If the filmed element had been in storage for the years since it was shot, like TNG, they would've held up fine. Like TNG, they would've had to done things like phaser beams and torpedoes in CGI.