A few quick responses:
1. Roddenberry's complaints about Star Trek II were pretty much based on the fact that Paramount had removed him from any position of authority for the movies. He was very unhappy about being shunted off to the side while Harve Bennett, a producer he had thrown off the set of one of his shows in the 60s, was given a position that Roddenberry still wanted. So, understandably, Roddenberry was ready to complain about pretty much everything in the movies after TMP.
2. The notion of Starfleet not being a military organization didn't start up until somewhere around TMP, as Roddenberry re-evaluated the series. Even in TNG there is a conflict in this line of thinking, since it's still clearly a military group. There are occasional bits of dialogue in TNG to say "We're really a scientific and exploratory organization" but the reality is that the Enterprise is always ready to defend itself and/or anyone else who needs it. At one point, Kirk tells Spock, "We're the only policeman on the block and a crime has been committed." Granted, Kirk also knows that armed force is not always necessary or appropriate. As he puts it, "We're not going to kill TODAY." But that doesn't mean that Starfleet doesn't have a fleet of ships that are quite well armed, and a corps of enlisted people and officers who have been trained as military officers. And we are regularly shown that Starfleet cadets learn battle tactics and maneuvers as part of their training, just as present day Naval Academy members do.
3. I don't have an exact number on how much Paramount spent on Star Trek Into Darkness, but I do know that they had a strong interest in trying to show that movie as profitable and successful in the public eye. Showing a budget level just under 200 million kept them out of the scrutiny that greeted elephants like Man of Steel and Lone Ranger. I frankly wouldn't trust any budget number from any movie unless I could actually see the numbers myself and what source was providing them. The production company's internal numbers would tell us that, and those guys are not about to let that kind of information go public.
But we're avoiding the real issue here as far as profitability goes. Tino is correct that the multiplier can vary between 2x and 3x the production budget. It can also be higher than 3x. One major variable is the ratio of the marketing budget to the production budget. In many cases, the studio spends far MORE on the advertising than they spent on the movie. One example of this is The Purge, which was reputed to have a budget of 3 million. Riiight. They spent more than a month in that house shooting for that low of a budget. A typical hour of network television costs at least that much and gets shot in 8 or 9 days. There's a major disconnect with the reporting of that number for The Purge, only some of which I can account for in terms of cast and ATL people taking very little money up front and deferring everything for points on the back end. Even past that issue for something like The Purge is that we know that Universal spent FAR more than 3 million marketing it - I'd estimate they spent at least 20 million or more on the U.S. marketing, given all the commercials, billboards, etc. And Universal made a tidy profit from the movie, even with the profit participants getting their cut. With the home video release, Universal should be able to instantly double the nearly 65 million the movie has already taken in, and that's without them having to spend any real money creating extra content for the Blu-ray or DVD.
In the case of Star Trek Into Darkness, I've tried to just be conservative and leave the production budget number at 200 million. I would easily add that number again for the marketing, given the blitz Paramount did around the world. (And the worldwide marketing paid off - this movie made more overseas than any other Star Trek movie and as a franchise first, actually did better overseas than at home.) The next 200 million after that is really covering two areas. One is that Paramount had to take out large loans to finance the movie. The interest payments on those loans over two years or more can get pretty steep, not to mention the other financial costs that get involved. Then you have the multiple profit participants taking their piece of the pie, which would include the whole gang at Bad Robot. And then you have the fact that Paramount doesn't get every dollar that comes in from theaters domestically or overseas. They get a falling percentage of the proceeds, with the biggest haul coming with the opening weekend. And you have to factor in that international distributors get their own percentage of whatever comes in, so that Paramount gets an even smaller piece of that pie.
So given how high the budget was, at 200 million, I really do think they were looking at needing to gross at least 600 million to break even. And I think they were hoping to do far better than that, given that they spent extra money to convert the movie to 3D, and given that they thought they had a great position for their release. Unfortunately, there were too many other movies out there that competed, and the real winners of the race this summer turned out to be Fast 6, Iron Man 3 and Despicable Me 2. Doesn't mean that Star Trek ID did badly by any means. It actually did quite well - better than any other Star Trek movie. But the budget was simply too high for them to be able to recoup without a superstar boxoffice performance. So they wound up falling short by around 150 million, which is about what we predicted would happen at the time.
The thing with Star Trek is that they can always make that money back with home video, and Paramount knows this quite well. I would expect them to easily make the 150 million back and probably do much better than that when all is said and done. But the hope is that they learned from what happened this year. And all that means is that the next Trek movie, and there will be one without a doubt, will need to be made at a more reasonable budget. Because if they had spent 100 million rather than 200 million on the movie, that figure of 450 million in box office would have put them way into the black. Kind of the same thing that happened after TMP when they reduced the budget to make Wrath of Khan. Khan was made for about 11 million, pulled in almost 80 million domestic, and that was before all the home video fun to come later. I believe Paramount will do something similar with the next Trek movie, and if they can just get a good script and a solid director, we may be in for something very nice in 2016 or 2017.