Well, a "best build" ?
It depends on what ship and class you are trying to use, for the "best" build.
And that is all dependent on your playstyle and what your team needs.
Well, for Modules ... If you are high enough level, Retaliator, Module Amper Fits your playstle module and then Adrenaline shot.
Those at this time at least, seem to be the best to use in almost any ship or class,Except for Corvettes, and Artillery cruisers ,Retaliator and Adrenaline shot ... Well, you probably will see no use in using them.
I listed Officer briefings, as ship loadouts vary so much by playstyle and what your team will need for you to bring.
So you may be good at plasma or purge ramming ...
Or love nuking ships.
Nothing is BAD ... Just not the best for what your team needs,Although you have to be adaptable.
If you feed the enemy team with a corvette 7 kills, maybe you should NOT feed them,So change to something to do good and for your team.
For Destroyers, you want things that synergise well, Storm Missiles and Torpedo salvo for example, Soemthing that you want to use ... When they have No shields and cannot evade the missiles and torpedoes.
For a Dreadnought, well most of the time Dreadnoughts end up in closerange brawler fights, CQC, so you want 1-2 abilities set aside for that, Pick something that works well together and with your playstyle.
[ Invictus is a little squishy for brawling I think. But it can be done still]
Artillery cruisers, You want to make sure you have 1-2 abilities JUST to kill off the inevitable corvette showing up in your face.
Something you like and can use well, also being able to be CLOSE enough to your Tactical so they can heal you and you don't feed the enemy.
Tactical Cruisers, well You can go one of four ways with that, 1.Pure healing,2.Pure survivability, 3.Pure damaging the inevitable corvette or plasma rammer coming for you, 4.Or Hybrid.
And corvette ... well I don't really know enough to comment lol
But they are the bane of disorginized not on Discord teams.
But you can attempt being sneaky sneaky with Cloak ... Only really works if no one is looking for it ...
But I think being more, fly in shoot, drop off an explosive torpedo shaped gifts and maybe securing a kill and running, is more of my playstyle, but I don't do good with it But others do !!!
Wyvyries mentioned building on strengths on ship classes and yes that is right, He used Building a tanky tanky Monarch as an example, and that is building on the strength of a ship to use it's full potential, But you also have to consider your team before you take a Monarch, or any ship, If you are in that tanky monarch for example, 80% of the time, the fight will be over before you get "to" the fight, and you just were able to shoot at range and not get in CQC, If your team is more speedy than you, you want to consider getting something that synergises well with your team.
But if your team is more Dreadnought focused, and the map supports the Monarch and you are able to use it properly,And you have a good Tactical cruiser to keep you up?
Then it's an awesome ship to play!