I do realize that things are far more complicated then the most of the simple ones want to realize and or rant about.
Technically speaking Cryptic is the "middle" man of sorts though they are shouldering most of the work.
Its more about numbers then anything. Make something that has mass appeal, relatively easy to play and charge a monthly fee. Star Trek as a large following, however I am willing to bet that a good % of that crowd are not mindless easy spending fools that will blindly waste 15$ a month.
I honestly feel that Cryptic could have done more if they really wanted to make that statement to Atari, if they wanted to make an in-depth product and they wanted to appeal to probably a smaller but more intelligent body. Other then just the "pew pew pew pew pew pew" mentality.
Make a quality product and the money/customers will follow.
I think the game is fine as-is (for a launch) and that Cryptic will work on more of the content that Trek fans want after the game is out and relatively stable. Just because people aren't getting it now doesn't mean they won't get it a few months from now.
Apart from that, I think ignoring the Trekkie crowd was the smartest decision Cryptic and Atari could have made. Looking back at the past fifteen years or so, if Cryptic and Atari had acquiesced to the Trekkies, it would have started a cycle where the devs would have had to more or less ask permission from the fanbase to do much of anything.