One thing, u say in your post, that once u reach certain part of the story line, i will get a free shuttle.. when is that?? i am already in the breen story line and i never got a free shuttle. I needed to buy one in the store because i needed it to do the vault mission ages ago. and i didnt like to skip episodes (and wth i imagined that i will use the shuttle more often but..).
So is that outdated, and now u will never get a free shuttle?
No, you still get a free shuttle.
If you were doing The Vault, then you should have gotten a free shuttle token with instructions to go pick one up at the shipyard. It doesn't automatically give you the shuttle, you have to go and buy it from the shipyard with your token. If you're a Romulan, then you should have gotten a free shuttle earlier on when you were doing the Rhi Atmosphere mission.
That said, the free shuttle is compete junk as I listed in the OP. You can buy a runabout class shuttle that's much better for Energy Credits in game at the shipyard (applicable for all factions). You don't have to buy a C-store shuttle at all.