It's a poor attempt at creating a money sink for the "economy." Aside from paying insanely inflated prices on the exchange for items (Which are usually inferior or equal to what you can trade badges for) there's not a whole lot/anything to spend EC on.
The saddest part is the shuttle itself is pretty lame compared to even the noob ship (1/2 the hull points and no rear wpn but more maneuvability) making it pretty much worthless for anything aside from touring the galaxy or mentoring Lieutenants when you're Admiral rank.
Make it some kind of "combat shuttle" with a turret slot in back, battle cloak, and higher ranking B/O slots, and it'd be worth picking up, even at three times the current cost.
I personally think the cost of these are fine, most people will pickup one when they at about RA Rank anyways and 150K of your account which would be at least a few million in credits is no big loss.
We use these in our Personal Fleet PvP events on a regular basis. Because there is not much in the way of ship ability that comes into play. It comes back to players ability to select the right combination of weapons and skills to succeed in this event.
Not everything needs to be about having the most powerful ship and having the highest DPS. Sometimes you just want to have a close fought team play orientated PvP event. These fit the bill very well.
These are a perfect example of trying something different that might just surprise you, if used in a different way than what your currently used to using in your standard ships.
I agree that Danube runabouts should be far cheaper, enough so to turn out being usable by level 3 to 10 characters as a possible alternate ship aside from the Miranda light cruiser.
Like, 5000 energy credits.
The ship is already a novelty as it is. I strongly believe that by reducing the price so, it would give it more purpose and functionality.
Heck, if they ever remake the tutorial/starter missions, having the player use a runabout as a training craft during a Starfleet Academy examination could be pretty swell. A couple of early assignments and poof, you get your starting light cruiser - maybe you even use the Runabout to fly up to it.
The Danube isn't supposed to be taken as a serious ship to fight in. This is probably the sole reason it is only for sell at DS9 instead of the ESD. Also...I'm pretty sure a shuttle craft would be no threat to a light cruiser, the best thing a Danube should be able to destroy is another Danube or a carrier launched fighter ship.