From reading the Ask Cryptic report I saw that they want to make the game more "Trekky" and I figure a great way to do that would be to provide missions where you have to save your own ship.

Examples:
Boarded by hostile race
Engines fail and your orbit is decaying
Power failure and must restore Warp Core (get to engineering via Jeffries Tubes n such)

And so on.

Is this something we could see in the future?

They've talked about this on and off. It's just a question of time for when they can implement it. Getting some ship interiors was the first step. More steps will follow. There's only so much manpower available for the mission design team, and most of them are working on the weekly series material.

Good call, thanks for the fast input. Really love to see how they are actually working on all our ideas and making a game that has the potential to have infinite replayability without the need to exactly add expansions.