OK, both rather unwieldy systems. Why is it, I wonder, that successive systems (aside from MgT High Guard version 1) versions of the game have made ship building more and more complex and difficult to work through (possibly rhetorical question!)?
Because the designers felt more detail was wanted/necessary.
The incongruities between Bk2 and Bk5 are enough to make most everyone itch, so having everything consolidated was likely desirable from the get go.
Then there was the impact of Striker, with its early approach to "build whatever" as applied to small vehicles would naturally get writ large to apply to starships.
Then you have the "simulation-ist" tendencies of the designers as they apply their wargame modeling expertise to something like an RPG. In the end, it was mostly just Chadwick refining his work over time until you get to TNE. He clearly enjoyed trying to successfully model "the real world" in terms of combat effectiveness in to a system that can, ideally, scale to the fantastical world of Science Fiction. "What should happen if a APFSDS-DU tank round weighing 20kg at traveling 1700 m/s hits a TL-15 Trader parked on the tarmac of a starport?" "What happens if the ship fires it's 150Mj laser back at the tank that shot it?"
"Giving these truths, and projecting these assumptions, we get these outcomes -- in a chart."
Arguably, the systems in TNE are actually very simple in that they follow the model of simply bolting boxes of systems together rather than any actual true integration. There's very little interdependencies. Most of the systems are designed independently and then drag and dropped in place. Notice there are no load balancing rules in FF&S.
TNE starship design is not that much more complicated that high guard. Grab a hull, armor it, grab a power plant, jump drive, and a maneuver drive, then fill the rest of the ship with rooms, fuel, weapons, sensors, electronics and crew.
In HG drives are built based on hull size. Given a hull size, TL, and performance desired (J-X, M-Y), and you get the size/cost of the drive. FF&S is the same thing. Power plants are built based on their output. Put in X MWs and TL, and get out a drive size and cost. Just like HG.
Where FF&S broke down when it came to ship design is that it did not include any weapons. HG included pre-built weapons: turrets, bays, spinals. FF&S did not. The basic book left those out. So, now you have to be not just a ship designer, but a laser physicist.
Brilliant Lances remedied this somewhat with standard turrets using "sockets" and some pre-built spinals.
Designing weapons in FF&S is, honestly, more involved than ship design.
The other problem with ship design is simply you had a gazillion options. "Gee, what size of diesel motor should I use with my Dean Drive given my 177 dTon hull made of cast iron?". If you stick to the basic TLs and basic components (fusion power plants, etc.), then all of that washes away with the noise. Same with the 2000 years of avionics history in the tables.
Now, obviously, FF&S added more things. Surface area for example (which I think was in MT already), abstractly manifest in HG as "100 tons per turret", the more complicated combat because of sensor rules (fire directors et al), etc.
But it was not an order of magnitude in complexity.
What TNE needed is what they published in Brilliant Lances. BL has the FF&S starship design rules. Barring errata, the BL design sequence is the same as FF&S one, it just focused on TL- 9-15 starships of the Imperium rather than all of the other stuff that was bundled with FF&S, and has a weapons list. So it's much more approachable. But it's all FF&S.