Adding +/- modifiers on weapons range/damage/speed/flux could achieve the role of "Rare Loot", but it would be a nightmare to manage. Unlike in M&B where you're the only person benefiting from a great weapon, or fantastic armour, your entire fleet is able to benefit from the gear.
Since weapons are already easily obtainable, having a negative modifier is probably not the way to go. Though having slightly better weapons, eg, Plasma Cannon with +10% Damage, +5 Refire rate, etc could add to the game, in that it gives people something to spend their cash on and strive for.
It'd also add a bit more of a feeling of attachment to certain ships, if they're decked out. Though that'd have to be combined with an option like M&B where there is no "Quit without saving" to avoid people reloading every time they lose one of those special weapons.
Another option could a research sort of option, where you can leave weapons you've obtained in a Research Tab on a space station for some cost, and every week or so, they gain an attribute (max of one, etc). Give people a way of upgrading their fleet at the cost of money, but making it a sort of "End Game" thing because of cost. Could set Research Assignments for stations that'd upgrade weapons with a greater propensity of the Assignment (Eg, Support assignments would result in more efficient, or higher ranged weapons, Assault might be Attack Speed and Damage, and Recon might give weapons cheaper cost to fire, and enhance secondary effects like EMP, etc).