- Decker - There are two Deckers to consider, actually, and they're equally viable candidates. The first is Matt Decker, who appeared in the original series episode "The Doomsday Machine." The second is Will Decker, who nearly replaced Kirk as captain of the Enterprise in The Motion Picture and was famously an inspiration for the later Will Riker in The Next Generation. More on both of them a little later in my not-so-secret bonus at the end of the list...
- Number One - The biggest loss from the original pilot to the original series, "The Cage," was the female commander played by Majel Barrett (the actress rebounded with two iconic roles, Chapel and Lwaxana Troi, plus the voice of Starfleet computers, of course, plus marrying the creator of Star Trek, Gene Roddenberry). This would have been a pretty historic character in the history of television. It's time she's given a second shot, and a name!
- Gary Mitchell - Some of the speculation concerning Benedict Cumberbatch's then-mysterious role in Into Darkness was that he was going to be this guy, an old friend of Kirk's who ends up with justified delusions of godhood who showed up in the second pilot, "Where No Man Has Gone Before." I think that could still make for a compelling movie character.
- Garth - One of a number of Starfleet luminaries to appear in the original series in later corrupted form, Garth was a brilliant captain who basically ended up suffering from PTSD, and was featured in "Whom Gods Destroy." Whether he appears in relation to Gary Mitchell or as a consequence of Admiral Marcus' shenanigans in Into Darkness, he could serve as a nice counterpoint to Kirk.
- Harry Mudd - A recurring character in the original series who even popped up in the later animated series, Mudd was obliquely referenced in Into Darkness already ("the Mudd incident"), although in the comic book prequel was gender-flipped. Fans don't seem as wild about him today, so he could use some redemption in the movies.
- Cartwright - Featured in both The Voyage Home and The Undiscovered Country, Cartwright was Admiral Marcus before Admiral Marcus ever existed, and seeing that both of them were heavily obsessed with the Klingons, who are bound to be featured in the next movie one way or another, that makes a natural fit for Cartwright right there, an attempt to succeed where Marcus failed.
- Chang - There are a number of iconic Klingons from the original series (Kor, Kang, and Koloth, who later reappeared in Deep Space Nine in one of the niftiest nods to continuity in the franchise), but Chang's role in The Undiscovered Country makes him more of a natural rival to Kirk, and it would be fun to see that revisited, while they're both in their primes.
And now my vision for the third film in the rebooted film series:
The story needs to be cyclical. I'm a sucker for literary storytelling like this, and a lot of that cyclical framework has already been built into the two previous films. Here's how it happens: Kirk and Carol Marcus once again have a baby together. Just as our intrepid captain is contemplating some well-deserved personal time, another crisis rears its ugly head. It's Decker, perhaps Will Decker the son trying to atone for the sins of his father Matt, obsessing over the the Doomsday Machine. Trouble is, the Klingons have noticed it, too, and like the Genesis Device of a previous movie trilogy, Starfleet finds itself in unexpected competition with the Klingon Empire (a nice echo, too, to the relationship originally featured in the series). Long story short, it boils down to Kirk having to make the same sacrifice his father did at the start of the first movie. In order to give his son a future he has to die. This was already teased in Into Darkness. The films could very easily continue with Spock as captain. And the kicker would be using the same music that serenades George Kirk's sacrifice as Jim Kirk does the same. Wipe tears, movie history achieved.