To give ideas to anyone who needs them, and get ideas from anyone who has them.

  
Vanilla. No mods. No cheats.  
Pic 1: overview, with the actual colors I'm using. I changed colors for the other pics for improved visibility because the lighting sucks in the ship builder.  
Last 3 images are 

1) my standard power distribution 

2) view from cockpit showing straight line to both ship exits, with beds just around either corner 

3) ship parked at Gagarin

Boosted stats (Reactor 46, Shield 1920) are from skill perks.

This build is not optimized for speed and maneuverability because that's not my playstyle. So I don't really care about the engines or the total mass.

Weapons:

W0: Vanguard Obliterator Autoprojector x 6 (requires completing the 1st vanguard mission)  
W1: PBO 175 Auto Hellion Beam x 4

W2: PBO 300 Auto Alpha Turret x 4

As recently mentioned in a post by someone else, the overview weapon stats don't really mean anything because they don't consider rate of fire. Not to mention other factors like the range and how long it takes the weapon to recharge/reload.

The turrets let me keep doing damage when I can't keep the enemies in my sights (especially helpful during the dogfight over Masada). They are positioned to maximize coverage in all directions, though there's still blind spots since they have limited range of motion. Putting them on W2 lets me avoid having to poke around to find the G key to fire weapons.

Other notable parts:

Shielded cargo + multifrequency scan jammer

Comspike and Conduction Grid (requires getting most of the way through the Crimson Fleet questline, but gives great combat boosts to your ship).

2 all-in-one berths for the beds. Viking CP-220 cockpit for 4 crew slots, and 1 engineering station (as the main hall) for an additional crew slot. 

Notable crew: Vasco and Omari Hassan for an additional 1 pip each to available ship power. Sarah because her Leadership skill gives you an additional crew opening, meaning you can add her to your crew without contributing toward your max crew capacity.

All interior space is on the same level in order to avoid interior ladders and make it easy to walk around inside my ship. To do this, you need one of the bays that can enter upward, and the slimline docker, inverted, right behind it. 

Behold, my mediocre end-game ship: The Veggie Pizza