Another thing that bugged me was the instance on military levels of discipline and adhering to orders, yet characterizing Starfleet as a non-military organization. Discipline is necessary for battle. If they are not a primary military organization, than they damn well better not be following orders blindly and strictly.
One thing I took away from this film is that Starfleet, and thus the Federation, has been having an internal dilemma during the period between movies as they debate the whole issue of militarization. The events of the first film, with a large chunk of Starfleet being annihilated and an entire planet, one of the founding planets of the Federation, being utterly destroyed would have led to much discussion of Starfleet's combat capabilities (or lack of). This increased militarization stemming from the events of the first film (remember, at least one entire class, if not more, at Starfleet Academy was wiped out in the first film in addition to all the ships lost fighting Nero) is probably why the dress uniforms seen in this movie have a more military look to them than other versions of starfleet uniforms.
With threats from the Romulans and Klingons already known, Starfleet can only assume that there will be other hostile species out there as we advance further into the galaxy. To leave Starfleet's ships as explorer only, with minimal weaponry, would be utterly foolish. But to arm the ships to the teeth, making them war vessels, would go against the Federation's principals of peaceful exploration. So the UFP and Starfleet have to walk a fine line between the two camps, a line that Admiral Marcus apparently chose to completely ignore.
I would guess that over the next several years, IN UNIVERSE, that this debate will become even more heated; the treasonous actions of Admiral Marcus an argument on one side (against militarized ships), but the recent destruction waged by Harrison/Khan weighing in for those in favor of more combat capable ships. What good is the Federation's Starfleet if it cannot defend the worlds of Federation from threats external and internal?
The Federation is going through a period much like what the United States went through after 9/11, a time of fear and concern, of rising need for improved military capabilities. And I think this trend could continue in further ST movies done by this team. I can even imagine this potential militarization leading to this alternate reality looking more and more like the "mirror universe" setting from the other Star Trek shows.
Yes, Abrams and Company are taking Star Trek into a darker future than previously seen, a future that is now quite unknown to us (although one can assume that the universe will try to course correct as it always seems to in the sundry Abrams'-universes, so who knows what the future really holds).
Maybe I'm trying to read too much into all of this, but one of the writing projects I've been working on lately (mostly for my own enjoyment and as an exercise) is trying to create a Star Trek show set in the Abrams-universe but during the time period (or close to it) of the Next Generation (ie the 2360s). So I've thought a lot about how the events of the first movie would effect the development of this new universe and the people and organizations that inhabit it. Add in the events of this movie, and I truly do think this universe is heading into a darker future than we have previously seen in Star Trek. I think it is likely that a militarizing trend is quite likely in this new universe, especially with the lessened influence of Vulcan logic on Federation policy (there are less than 6000 Vulcans left by Spock's estimate in the first film, a population that is not likely to be large enough for a viable gene pool) and the Vulcans now have greater concerns than the Federation; they have their entire culture to preserve at this point. So I can imagine that the influence of the more militant Andorians becoming greater in the Federation Council and in the command staff of Starfleet.
