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Answer from: BrysolMarque
The answer to that question is rather complex. So be prepared for a very long winded answer. I understand that the original poster may never actually read this due to the age of the question, however I would like to lend my experience to other would-be space pirates who happen to stumble across this page.
In my honest opinion (tested and verified) every ship type has its purpose and therefore can potentially be the "best" ship to have depending on how it's built, how many ships are in the fleet and where the fleet is placed in the armada. Due to each weapon "mainly" targeting a specific fleet (Biggest, Smallest, Figurehead), you may want to have a very LARGE fleet of cheap cruisers with Cannon (mainly attacks largest fleet) Resistance stacked to take the brunt of the Cannon volley and still have a sizable fleet for the battle itself. Perhaps having a smaller fleet (not small by any means, but the smallest fleet in your armada) with Missile (mainly attacks smallest fleet) Resistance stacked to direct most of the missile damage to a properly prepared fleet. Beam weapons and Fighters both attack the figurehead fleet mainly, therefore having your first fleet stacking these two resistances will prove to be useful. Opinions on weapons load-out vary from pirate to pirate, I tend to mix/match weapons on each fleet to better utilize the dual bonuses.
Most ship parts come with a specific set of bonuses. For instance, the Electronic Storm Device gives you bonuses to both BEAM and CANNON attack power. Therefore having a fleet equipped with both types of weapons will not only enable you to participate in the entire battle (Cannon is preemptive, the Beam will be used throughout the entire battle), but also maximize your bonus for BOTH weapons.
Each weapon and ship type has a purpose, therefore a decent assortment of both will give you the best results in combat. READ the information for your ship components and the ships themselves. The game specifically tells you what each was designed for and what it works well with.