This sounds like great fun, and about time, too. Given the fact that the next movie is apparently a leisurely process, it's nice to open up on a version of Star Trek that's practically a gift for any ambitious enough fan to play around with, in terms of story ideas. I'm not even to preoccupied with if they explain where the new version of WNMHGB is going to happen chronologically, given that the new Captain Kirk seems to have taken command of the Enterpise 5-7 years before he did in the original continuity. As long as they try to be creative enough with it.
I don't want to suggest that the new vs. old Battlestar Galactica's are the perfect example for how they can really make this work well, but there are good ideas there. Obviously, the tonal shift of that franchise wouldn't be appropriate for Star Trek, but our new understanding of the Enterprise crew's character dynamic could have a satisfying impact on how a story will turn out differently, and that's without taking into account how events have changed from the ripple effect of Nero's incursion. The new Galactica show was good about taking an idea from the old show, and playing it out for the length of time that seemed appropriate. The old episode with the raging fire on Galactica becomes a five-minute crises situation in the new show's first story, the old show's two (or arguably one) part Kobol storyline stretched into a nine episode storyline in the new version, and a 20-30 minute segment from the old show's first story is cannibalized into an episode all of it's own in the new series. And that's just a superficial breakdown of how a story is rejigged.
It might be interesting to eventually really push the envelope in terms of believable conundrums. The new Battlestar show took the idea of The Drumhead episode from ST TNG and played it out in a different way, particularly the resolution (admittedly, the finale results from very different circumstances, but then, the new ST continuity is a new set of circumstances, too). What if after they encountered the Guardian of Forever, they continued the story to show how the Federation and Starfleet deal with a very serious security concern? Because Enterprise is on station at the Guardian's World, they would be the people to keep there for a bit longer as security arrangements are made (the less people that know about it initially, the better). Then, what happens when security is breached? Should the Enterprise hunt down and kill a Romulan or Klingon starship that scouts out the planet, and then does a runner for home?
There's also this fun game that some writers play, taking old story ideas that fans traditionally consider rubbish, and turning it into, say, a genuinely menacing villain, or a better thought out concept. Reconceptualizing garbage into a Philosopher's Stone.
Then there is the stuff that is great, that you could make more out of. I know some people think that Khan is overplayed, but I think there is greater potential. Instead of an exiled superhuman and his followers, stranded, what about making him a political force? I would like to see Khan as a warlord of a conquering horde, who learns to play clever political games when he comes into conflict with the Federation. So many rematches between Kirk and Khan (just as long as it doesn't get overused like something that really was overused, like the Borg).
One thing worth looking into is the world of Bread and Circuses. Good story, with one major problem at the end: why in the hell would they leave just after the moment they discovered the possibility that that planet was experiencing the coming of Christ?! No, I'm sorry, but no. They are explorers, for heaven's sake, and the event they stumble upon at that world is one of the best reasons for exploring. That is an unprecedented opportunity, and the Enterprises cameras should have been recording and copying all the data it could register coming off that planet.
Garth of Izar seemed to me like a character with greater potential than an insane asylum inmate that must not be allowed to escape. To me, he could represent that the opened mindedness that explorers need in order to understand other cultures, but gone horribly wrong. He could be an expression of the darkest side of moral relativism that helps to understand the strangeness of other cultures. He's travelled so far, but his experiences have changed him, so that now he's the one who has become alien in thought and action; a warning of psychological dangers (I don't mean in a Heart of Darkness kind of way, although I can see how this description could look that way).
One thing that really troubles me, though. If it's okay for the comics to finally take advantage of this new version of Star Trek history, then what is going to be the story with those unpublished novels that were supposed to be set in the new continuity, which were pulled from the publishing schedule? If it's okay for the comics, can they not, now, finally release those things? I was going to buy those books, and it was at a time when I was having to resolve myself to be more picky about the books I was buying! There shouldn't be any reason to hold back with those novels now, I would hope!