[X] 0: No Shuttlebay
[X] 1: Transporter (+10,000 Tons)
[X] 2: Cargo Bay (+10,000 Tons)
[X] 3: Brig (+10,000 Tons)
[X] 4: Tractor Beam (+10,000 Tons)
With the core systems decided, you evaluate your progress. Your design will mass the most out of all the entries at one hundred thousand tons, a hefty build that may be a mark against you during the procurement process. Losing the shuttlebay may potentially limit the ship's utility in less developed areas, but given the design is primarily focused around servicing the member worlds and major colonies where other vessels are likely to be available it represents something of an edge case for capability loss. The extra mass you save and not needing to plan for a shuttle hatch simplifies some parts of the design tremendously.
Now comes the matter of the hull. There are several configurations you could use, ranging from a saucer with a fully integrated deflector to a more traditional primary and secondary hull. Being constrained to one impulse engine limits you somewhat, excluding the possibility of an arrowhead, while the phasers demand a wide field of fire that makes a more cylindrical profile suboptimal.
The first option is the full saucer with an integrated inline deflector. This would allow you to make the main body of the ship quite large, leaving the nacelle to be attached to the primary hull by a standard strut. Or you could separate the deflector from the main body to a secondary hull, keeping the shape of the saucer more consistent and keeping the design more centrally balanced between the engineering section and nacelle. Finally you could use a half-saucer, opting for a larger secondary hull in exchange. It's an odd feeling, planning from an aesthetic rather than a functional point of view. Such a straightforward and simplified design lets you play around with form without compromising much in the way of function.
[ ] Full Saucer with Inline Deflector [Total Mass: 100,000 Tons]
[ ] Full Saucer [Primary Hull Mass: 70,000 Tons] (Secondary Hull - 30,000)
[ ] Half-Saucer [Primary Hull Mass: 50,000 Tons] (Secondary Hull - 50,000)
Two Hour Moratorium, Please