My first shot at a Spacedock vessel, this is a limited issue vessel used at 98% by Starfleet Intelligence and Section 31, with the rest in the hands of scout capital ships. For an idea of what it looks like, I had the idea while looking at the Type 12 shuttle in the journal of treknology part of ex-astris-scientia. From the possible dimensions, I managed to make something nearing the size of Voyager's type 9, which I feel is about the biggest you'll fit in a Nova shuttlebay (everything I design or modify has either the Nova/Defiant/Sabre or the Steamrunner/Intrepid ships in mind, sometimes with a thought for the Sovereign) without requiring a shoehorn to get it out of the shuttlebay.

Class/Type: Type 12 Covert Operations shuttlecraft
First Commissioned: first fully operational test vehicle launched in April 2372 from USS Ophelia

Hull Systems
Size: 2
Length: 9.1 meters
Beam: 5.2 meters
Height: 2.12 meters
Decks: 1
Mass: 1.8 metric tons
SUs Available: 500
SUs Used: 480
Hull
Outer Hull
Inner Hull
Resistance
Inner: 4
Outer: 4
Ablative Armour: 100
Specialised Hull Options
Planetfall
Atmospheric Capability
Energy Sheath
Structural Integrity Field
Class 1 (40/60)
2 Class 1 backups (20)
Environmental/Personnel Systems
Crew/Passengers/Evac
1/8/10
Seating for 8(120/SU)
Basic Life Support
Reserve Life Support
Emergency Life Support
Gravity
Consumables: 1 week's worth
Jefferies Tubes
Fire Suppression System
Propulsion Systems
Warp Propulsion
Type 5 encased nacelles
Type E PIS (8 hours)
Warp Speeds: 5/6/6.4 (Max Warp downrated by .4, cruise and max cruise uprated by .1)
Impulse Propulsion
Class 4 Impule engine, Beta Acceleration Package
Impulse Thrusters
Speeds: .7c/.9c
Power Systems
Warp Core: Class 4/G MkIV
Fusion/Impulse Core: 32 power
Auxiliary Power: 6 reactors
Emergency power: Type A
EPS +80 transfer
Operations System
Cockpit
Computer Core
Optical Data Network
Navigational Deflector
Sensor Systems
Long-Range Systems
Type 1, Strength 4
Lateral Sensors
Strength 4
Navigational Sensors
Strength 4
2 probes
Flight Control Systems
Autopilot (Skill 1, Co-ordination 1)
Navigational Computer (Class 1) and 2 backups
IDF, 2 main and 2 backups, strength 6/4
Attitude Control
Manual Steering Column
Communication Systems
Strength 4, Security Uprating Delta
Transporter Systems
Type 2 personnel transporter, 8 pads, Class F E/T Coils
Masking Circuitry (if you consider it as a breach of the Treaty of Algeron, make it a class Delta Hull Holo-Emitter, 12 SU and 90 power, performs as a Class 2 cloak with a slight bonus)
Security Systems
Anti-Intruder System
Internal Force Fields
Tactical Systems
2 Phaser Arrays
40 Type V emitters, Alpha Interlock, 180 degrees arc, Continuous/Standard/Pulse
Micro-Torpedo Launcher, 80 Micro-Torpedoes, Spread 5
Class Alpha TA/T/TS
Deflector Shields
Class 2 Generator, Beta Distortion Generator, Class 1 recharge, 4 backup generators
Protection 210 (+100), Threshold 70 (+10), 9 rounds recharge
Self-Destruct System

"We are explorers, we don't sneak around". Cute saying, but it is not what we think at Starfleet Intel, or at Section 31 for that matter, but it helps for the public relatios to have Starfleet use this as their official policy. This shuttle is an improvement from an already existing low-profile shuttle design used by Starfleet Intel, but in times of war, where what you are hunting down boasts more powerful sensors than your average pirate, it always helps to have something to keep hidden from them while you are scouting for the big ships. This is why the SIR&D have decided to research for other ways to have stealth technology without breaking the Treaty of Algeron. This shuttle is almost unknown of outside of either the admirality or intelligence, and even for those who know about it, they rarely know their full capabilities. If they are issued to your ship, it usually mean that your conditions are going to be almost as bad as if Starfleet Command gave you Q-torps as standard onboard. The uses of this craft are the stealthy deployment and retrieval of black operations squads, some use it to scout around their ships due to their stealth options, and some even use them to raid lonely and small targets with a flight of these, changing their two probes with a pair of fire-and-forget torpedoes.

Not to be issued in great numbers, I personally tend to give only a few to my players, and they are told before, this is NOT a red shirt shuttle, you won't have as many as you want, their systems are very sensitive and hard to fabricate, while a couple of parts from their systems can't be replicated due to delicate alignment problems or materials (they asked me why, I created a molecule with 2 latinum atoms in it, made it a part in one of the components, they don't bother me anymore, they know I mean it when i say HARD TO BUILD). IMO, ships shouldn't be issued more than 6 unless the CO is a flag rank officer part of Starfleet Intel or Section 31. All systems fit, if my double, triple, and quadruple checks are OK of course .