4. Not so much an FX comment, but the new editing technology does not seamlessly match the dissolves from the oriignal production. In otherwords, the transition from TOS footage to new FX looks very much like any video edit job of today, which takes the viewer out of the moment.
In defense of #4, the issue they faced was that all that remained was the completed episode on a master 35mm reel in the Paramount vaults. So to make a replacement shot, they had to make the new VFX sequence go a split second longer than the time the original VFX shot took, so yes there's often a noticeable sort of cheap "time edited for syndication" look to it. CBS-D said they had no choice, and hated that it kept turning out that way despite their best efforts.