This is a two part idea, because I see there are shuttlecraft in the game, but no real uses for them.
First off, the shuttlecraft at DS9 is awesome, however it would be nice if there were specefic missions that could only be accessed by owning one. For example a nebula or debris cloud you can't fly your starship through. A planet that can't be beamed down to, and you have to have or atleast own a shuttlecraft. Shuttlecraft PVP arenas.
Also, most starfleet ships have shuttle bays where they have several shuttlecraft inside. I like the "carrier" idea for the klingons and think that should be expanded. I think based on the rank/class/size of your starfleet ship you should be able to have several shuttlecraft. For most basic ships, they should atleast have one that they can deploy.
Idea: you buy your first shuttlecraft which you can fly around, customize, etc. This adds a shuttlecraft counter to your ship of 1. This first of all opens up additional mission types where shuttlecraft are necessary. This also enables you to launch atleast one shuttlecraft while playing missions or pvp'ing.
If you have larger cruiser or carrirer style ships, you can buy additional shuttlecraft which adds additional counters to your ship (up to a maximum level). This would allow larger ships to deploy more shuttlecraft.
Various types of shuttlecraft or runabouts could later be added with different benefits or enhanced abilities.
The shuttlecraft was a vanity item and was always meant to be. I understand your attempt to get it into the game in a more active role but it's just not practical. I own one myself but it's just for show or the occasional low level deep space encounter when i'm bored.
I think the only practical way to get it into the game and make it useful would be to make it a customizable combat pet. On the klingon side give them a fighter craft or something to be identical. I'm not sure how you would rationalize that for klingon ships but.. yeah.. it might work.