What if instead of doing a new timeline they had shatner and and Nimoys Kirk and Spock turn into a younger version of kirk and Spock and the same with the others? like Doctor Who>?
That would still leave all the continuity issues with the previous Trek which the new producers were trying to avoid. Also, Kirk is dead. The rest of the crew, if they are alive, had 70 years of not-serving-on-the-Enterprise-under-captain-Kirk (except Scotty...). Why would they band together? I don't think Uhura would like to be back answering the space phone.
Several years ago, I decided (all in fun, of course) that this is why Saavik in Star Trek III and IV looks and acts nothing like Saavik in Star Trek II.
Opening scene of Star Trek XI: SPOCK: "Chekov, Uhura, Sulu. Thank you for coming." SULU: "It's our pleasure, Ambassador. But why have you insisted we come to the Genesis Planet, and also bring along the remains of Captain Kirk, Scotty, and Doctor McCoy?" SPOCK: "Because my nemesis Nero has threatened to blow up Vulcan. We must reanimate Captain Kirk and rejuvenate his best crew to stop this tragic event from occurring. Let the metagenesis begin!" And then the whole movie is in 2387, but they all dress like the alternate reality and the "Abramsprise" is actually the Enterprise-F, built in secret by Spock.
Okay, how about cloning, thanks to Section 31? It would be like in that Justice League Unlimited episode, called "Epilogue", where Amanda Waller of Task Force X (ie. Suicide Squad) decides that the world always need a Batman, and decided to clone Bruce Wayne (by over-writing a couple's DNA), then tried to set up the exact same events that led to the the deaths of the original Batman's parents. Perhaps, in the 25th century, with increase threats to the Alpha Quadrant, you will need a Kirk and crew who can think outside of the box when dealing with threats. Of course, though clones, they wouldn't be named after the original crew, or even have the same sex, but would be put into similar situations in order to bring out what made the original crew legendary. Of course, this crew would find out about the truth, have a crisis of faith, and then overcome their trauma to forge a path of their own.
Pass. While I find the new movies a lot of fun and entertaining, and it's something that's never been done within the franchise, I don't think we need further suggestions that the universe will fall apart without Kirk and Spock.
So in order to retain the character templates you're suggesting that these human beings *regenerate* ala Doctor Who. Like a Time Lord. Which they are not. Gotchya.