I fear you so much concentrated on the comparison with EVE that you lost most of the connection with Freelancer.
The ship class breakdown is rather useless, it essentially says: combat ships are good for PvP and NPC killing, transports are good for trading and NPC killing... and the point is? There's much more to the ship classes, with relation to other ship classes.
Most often ship class is determined by the specific purpose of the ship, unfortunately I would never even imagine defining it by the terms you use. I want to survive, I take a nimble fighter. I want to kill caps, I take bomber or another cap (but there the choice depends on multiple factors). I want to be a strong weapons platform, sacrificing the ability to avoid taking damage, I take a cap.
When the ship class is determined, most of your loadout "choices" are determined. Scanner is determined for all of them anyway.
The ones determined by ship class:
Shield class
Armour (on caps it depends on your purse capabilities, still not mission-dependant)
Thruster
The only class that really chooses an armour upgrade depending on preferences is a Transport. It can choose a cap armour for high bonus and reduced cargo (and consequent profit reduce) or a universal armour bonus with less cargo taken and smaller bonus.
Shield type - well, there can be some choice, but most it won't depend on NPCs. In most cases you can defeat them regardless of your shield type (or can't defeat them regardless of your shield type), what really counts is player opponents. Pulses still have a slight disadvantage against Gravitons, that makes them the most popular choice. If you are going to face Outcasts, Molecular shields are a good choice though (against Particle Krakens).
We have a bit that could be left! Or at least edited to that effect at least...
Your guns: One point that's valid there - you can go for top damage and go with aimed shots or some balanced damage/power ratio with reasonable power draw (having no draw would be just a waste).
Then there is the huge and complicated area of capital ship weapons...
Carrying extra ammo for the fleet or donating bots/bats in fight doesn't have much to do with the choice of a ship or equipment, unless you're getting a Repair ship.
If I was to edit the article, there wouldn't be much left. So I'll just stay at disagreeing with it almos completely. There could be an article about loadout choices, but this isn't the right start.
