I think Cryptic would have recieved far less backlash and far less general grumpiness about the C-Store, had they approached it differently.
"How should they have done it then, Mr. Smartypants?" you may ask.
Well, given that:
Captain Matt Schwab presents:
How the C-Store SHOULD HAVE WORKED!
1. Canon is core.
What does this mean? Simply put, if it is canon, then it wouldn't have gone into the C-Store. Let's talk ships for example: I would have made all the canon ships available in the game, in their default appearance and configuration. Period, no exceptions. Then, I would have made the "Cryptic" ships and any alternate variations like Galaxy X purchaseable from the C-Store. So, from the base game, you would have all the canon ships, but in terms of customization, you wouldn't be able to change much except for colors, patterns, window types, etc. If you want to cutomize your ship further, you would then go to the C-Store, purchase the ship(s) that fit the ship type you fly, and then you would have the ability to kitbash unlocked.
So, for example, the Galaxy class would exist in it's TNG default configuration. To customize it, you would buy either the Celestial or the Envoy (or both if you wanted) which then allows you to change your hull, nacelles, saucer, pylons, etc.
2. Canon is core, Part II.
In terms of uniforms, you would have access to all the canon uniforms from all the series and movies. ENT, TOS, TMP, TWOK, TNG, DS9, VOY, Nemesis. Anything else beyond that, including the Cryptic variations and Mirror Universe uniforms would be purchaseable.
3. Canon is core, Part III.
In terms of equipment (Weapons, Tricorders, etc.) all the skins used would make your equipment look canon. you would have access to 5 eras of equipment to choose from. ENT, TOS, TMP/TWOK, TNG and DS9/VOY/TNG Movie. If you want the flashy honkin space guns, then you would purchase a weapon skins pack from the C-Store.
That's it. That is all there is to it. Anything which is canon goes into the game for free. Then, it's up to Cryptic to develop the items which reflect the new era in such a way that it makes people want to purchase them. That satisfies the people who don't feel they should be paying for fan favorites, and it still gives Cryptic a chance to make a profit on people's desires to be unique and customize their avatars!