Casting
So in addition to Persis Khambatta joining the crew in her role of Ilia, which would later transfer to Star Trek: The Motion Picture, you also had the part of Commander William Decker. This part was never cast during the production phase of Phase II, but the roles were pretty much the same in the later film. You might also know more about how the two were intended to interact by watching Star Trek: The Next Generation. You see, Decker and Ilia later became the basis for Deanna Troi and William Riker (originally Ryker). Although in Troi's case, I don't think they ever planned to shave Marina Sirtis' head. Also, the Kirk/Decker relationship was intended to be something akin to a father/son bond. Plus, although with Number One in The Cage only being referred to as such being the obvious source for Picard later calling Riker the same it was actually the intention that Kirk would call Decker "first" as a nickname. Considering the re-use of the character with regards to the Decker/Ilia relationship, I wouldn't be surprised if this was also the source of Riker's nickname.
The third character the science officer didn't cross over properly into the later film as he was replaced by the return of Nimoy. But for Phase II, David Gautreaux was cast as Xon. The character was Vulcan, but unlike Spock, he was intended to be a full-blooded Vulcan. He was also to be much younger than Spock, but a genius. The 1977 writers/directors guide for the show explains the difference between Xon and Spock better than I can:
Xon realizes that the reason that Spock performed so well in his tasks on board the Enterprise was that he was half Human and therefore could understand emotional Human nature. In order to perform as well as Spock, he knows he is going to have to eliminate his Vulcan revulsion at emotional displays. He is, in fact, going to have to reach down within himself and find the emotions that his society has repressed for thousands of years so that he will have some basis for fully understanding his Human associates. What this means is: whereas Spock was engaged in a constant battle with himself to repress his emotions in order to be more Vulcan-like, Xon will be engaged in a constant struggle within himself to release his buried emotions to be more Human-like for the sake of doing a good job, his primary considerations. This will be at least as difficult for him as it was for Spock to maintain his stoic pose. Also, we'll get humor out of Xon trying to simulate laughter, anger, fear, and other Human feelings.