Here is one reason I think it might be in the prime-timeline:
The release date.
It's 2017.
It would be much smarter to bring out a new series in 2016, for it's 50th anniversary. So why put it in 2017? I got the sense the reboot was originally planed as an entire new continuity, with new shows set in it and all of it. 2016 is the third installement of the reboot movies in cinema. There was probably a contract, that if they were to produce a new series in the timeframe of the 3 abrams movies, bad robot needed to be involved. Instead. A 4th movie is already announced, but as you saw, all contracts needed to be re-negotiated (that's why it was announced so ig that Pine and Quinto would appear in the new movies). It's likely CBS will wait until 2017 to be allowed to make the series without bad robot, but put it as soon as possible (january) for general audiences to still rember the big anniversary.

Other thoughts:
- Seriously, bad robot is not involved. Which means, JJ abrams is not involved. And those are the guys that have the rights to the JJverse
No. Paramount owns the copyright to the films themselves. BR owns none of it. But again, CBS owns the characters, the trademarks, etc.
- There are practical reasons to put it in the new timeline, namely:
i) the JJverse spaceships are much to big. They need giant sets, and props (like shuttles/torpedoes) are enormeous. The old continuity is much more television-conform
Ah, the wonders of green-screen sets and CGI in those cases.
ii) Kurtzman seems to be the only one involved from the JJ-crew. And he's the guy already working for CBS. So for CBS it would be a smart move to put him in charge of a new series, that would look and feel like the reboot, without being officially part of it and the need to negotiate with Paramount over license fees
Again, CBS owns the trademarks, the characters, etc. Also, the blu-rays of the new movies? They are produced by CBS and Paramount.
iii) There's a fourth movie planned. Which means a new television series would need to be heavily synchronized with the movie staff, to not contradict themselves. If it's all under one parent company (like Marvel over different mediums) it would be possibly. But the series is produced by Kurtzmann's own production company. The only alternative would be to put the series in the JJverse in tha past (which would be a prequel, unlikely), or in the far future a la TNG. And then there would be no benefit to put it in the same continuity and be heavily bound by events of upcoming movies
I don't think that's the only alternative. The fourth movie also isn't due out for another four years. Plus, may I remind you that DS9 and Voyager were synchronous with three of the Next Gen films? And they did just fine.
iv) The JJverse offers nothing new: warp drive, shields, beaming, klingons, vulcans, phaser are the same in both continuitys. The only addition of the JJverse canon-wise are stupid things like "transwarp-beaming"
Your point?
v) The JJverse is not long-time sustainable. It's basis are Kirk and Spock. Maybe after the 4th there's a 5th movie. But after that, they need to either re-cast or re-boot again (because they will NEVER EVER make a summer blockbuster with a new crew originally from television). So why set it in the new verse when nobody know how it will end, and you have all creative freedom to go on in the old?
Then they reboot. How many Sherlock Holmes have they had? How many James Bonds? How many Supermen? Spidermen? Batmen? That does not worry me in the slightest.
So, all in all:
I hope it's not set in the JJverse. What will happen instead?
It will look like it's set in the JJverse. In the first few seasons, they will probably leave all possibilities open. It will be set on new worlds, and neither Vulcan nor Romulus will be mentioned specifically. That means: It won't be a sequel to the TNG-timeline either. No mentioning of the Dominion War and stuff apart from side remarks. Although it is possible to have guest appereances by old actors, like Patrick Steward or Jery Ryan. But don't expect them until the series stands firmly on it's own foot.
All in all: Probably, hopefully, set in the prime timeline. But it will resemble the prime-timeline as much as TNG resembled TOS.
I think it is highly unlikely that they will return to the Prime Universe. Why? Because there is over 700 hours of constraining canon to consider. Setting it ahead another century or two does nothing except give more excuses for technobabble galore.
What do I want? I would prefer to see a completely new universe. I'm serious. Let the films have the JJverse. That's fine. But let's not have any constraints. They shouldn't be beholden to the idea that the Romulans didn't have cloaking devices or that they only had subspace radio during the Romulan War. That's crazy! Going back to the Prime Universe is looking back. Star Trek is about looking forward. And if it is set in the JJverse, that's fine. But I would prefer something new. If it's set in the Prime Universe? I don't know that I would be interested.
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