I have no clue why the pulse laser is supposed to be better. It seems extremely marginal, especially considering its higher power cost and LOWER penetration values. It does do a bit more damage at the same fire rate. It also might have a faster projectile (not sure if this helps or not).
As for armor, fighters usually have pretty bad hull values. A single Fighter 3 armor will increase its health almost 50% or more. More importantly, when a fighter DOES eat a stray shot or two, its better to have armor take the hit and leave your systems intact. Eating an engine hit is pretty much game-over.
As you mention the speed hit is relatively minor and the major problem is that armor is so freaking expensive.
I believe the hit formula is somehthing like: (Speed of Target / Speed of Tracking Weapon)*100% = the speed portion of the equation. This is only for targets SLOWER than the tracking speed of the weapon. Otherwise, it CANNOT HIT except for a 3% (or 2% i forgot) lucky shot chance.
Note that the size of the craft matters too. It is basically (Size of Craft / 256)*100% (cannot go over 1 I believe). Both the Speed factor and Size Factors have a 50% weight (i.e. divide each by 1/2 and add em both together).
For fun testing, try a 2.7 speed fighter with armor, vs a 2.9+ish speed fighter with no armor and see what that does for ya. In theory, the 2.9 will be all but unhittable by the 2.7 fighter, whereas the 2.7 will have about a 55% chance to hit, based on speed-factor alone.