system
Given the following post, respond as if you're commenting on Reddit:
human
[Star Trek] Starfleet has one of the weirdest ship designs with a saucer/engine setup. Even a battleship like the USS Vengeance uses this mold - they simply don't look sturdy. Is this an aesthetic choice humans made long ago?
gpt
The main advantage to the split-hull design is one of safety, by separating the primary crewed section from the engine areas, it improves the survivability of the crew in catastrophic scenarios (such as a warp core breach). The engineering section is shaped as a cylinder as a space-efficient way to wrap all the bits that need to go there, while minimizing exposed surface area and "blind spot" it causes to the saucer section.

The saucer section is a tapered disk as a way to maximize the visible arc of any sensor (or weapon) placed on its surface, and increase available surface area, without needlessly adding the volume/mass that a spherical crewed section would have (also minimizes the exposed cross section from the front/side, at the cost of increased exposed area at the top/bottom). Also having wider levels may be more desirable for some purposes than having more levels stacked on top of each other.

The nacelles are then located the way they are as a way to maximize the efficiency of warp travel - ideally you want ~two nacelles placed outboard of your ship that have line of sight with each other; though many other ships accept some sort of inefficiency in favour of other design considerations. Other ships also forgo the split-hull design in favour of designs with different tradeoffs (it's only really practical to do on larger ships, it's cost-inefficient, it necessitates a larger overall ship design, increases travel time for crew between positions, etc).

Ships like the USS Vengeance keep the same design, largely because it's a familiar design to Starfleet shipbuilders - they know its tradeoffs and limitations, so they know how to work around them. Trying to build a ship around unfamiliar design principles is asking for trouble, especially when you're trying to do it in secret and thus can't spend years on R&D and dozens of test vehicles. Also some parts/designs may have being created by people not privy to the secret of what the USS Vengeance actually was, so making it look like a traditional Starfleet ship helps prevent suspicion.