I don't see how upgrading the movie's effects would be profitable.
Neither does Paramount, otherwise Shatner and a CGI team would have been thrown into a room together years ago.
It's a shame, I'd love to see Shatner's original ideas finally on film. I'd be much more inclined to buy a "definitive", Shatner approved TFF with CGI than see bits of TOS episodes interspersed with 2000's CGI.
Oh, and to the guys doing the fan restoration - great stuff