Yeah, I've seen this before, years ago, right?
I think the premise is wrong. The decline in Star Trek's ratings are not simply a function of the content of the series. It's part of an overall trend in entertainment that has occurred since the glory days of TNG. Ratings for everything is down. Shows are "hits" with 10M viewers. Out of a nation of 300M, that's 3% of the population watching that so-called "hit" show.
Blame the profileration of media channels - more TV, DVDs, video games, the internet. There is far more stuff out there than people to consume it. Entertainment therefore has split into two survival strategies: the truly lowest common denomenator stuff - reality TV, formulaic cop shows - and entertainment that serves some niche so well that the niche stays loyal, buys DVDs, etc. Sci fi by definition belongs to the niche strategy.
If JMS wants to re-boot Trek, he should just come up with a good idea, that will appeal to a niche audience (maybe the existing fanbase, but maybe not). But he should not assume he will get anything more than a niche audience. 10M viewers would be just fine - and yes, that is a niche. 3% of the population is not anything like a mass audience.
The concept of re-casting Kirk, Spock and McCoy is actually a good one for serving this niche audience which will most likely be a mix of Trek fans and new people. And it will alienate other Trek fans. So be it. A niche means you can't please everyone.
But then JMS goes off the rails with that "ancient mystery" stuff. That's more B5-feeling, not really very Trek. Star Trek isn't about mystical hooey, it's got to stay centered on the political philosophy that underpins it: that liberal democracy will expand throughout the cosmos and even if there's a whole lot of fighting along the way, eventually everyone will be friends under the benign eye of the Federation, with Starfleet as its muscle. That kind of imperialism-for-democracy is Star Trek's "thing," what makes it unique, and that is the element that at some level must always be present.
I don't expect Kirk to "win command" of the Enterprise because he's pursuing an ancient mystery. I expect him to do that because he's got an unparalleled genius for the job - and whatever the mission was that allowed him to display that genius is irrelevant.
Kirk wasn't just given command of the Enterprise so he would wander around aimlessly. He, and everyone else in command of a starship, has a general mission to patrol and defend the Federation. Look at the actual premises of the TOS episodes. Kirk was always checking on colonies, ferrying diplomats, fighting Romulans and Klingons and the odd Doomsday Machine. His role is soldier and cop, and when he has time, he can do some exploring. That role is sufficient for any amount of stories, we don't need to create some goofy mystery at the center of the universe to give Kirk something to do.
JMS's plan doesn't convince me that he understands the core of Trek. It's like he's trying to re-make B5 and slap the Star Trek label on it. If JMS wants to create a series with a Priest, Warrior and Doctor who goes off finding ancient mysteries, he should go right ahead. It won't be Star Trek, but there's no reason it has to be. Call it something else, cast it well, write it well, give it a decent production budget and put it on TV. I'll give it a fair try-out. I can enjoy shows that have nothing to do with Star Trek.