ok, so word on the street it seems is that missiles are still the best due to the first strike ranged attack ability. kinetic being 1 stronger and beams being a little cheaper while having 1 less dmg are both still not worth that ranged attack ability. so here's a quick fix i recommend to switch things up a little more to help even it...
Missiles: have the best special ability, so they should have the weakest attack. base 2.
Kinetic: strongest attack, weakest or no special ability. base 4.
Beam: med attack, low cost. base 3.
derek suggested a repair debuff with kinetic weapons i like too. while minimal in impact, it would help give that weapon type a little more flavor, and help it be a better offensive weapon. if implemented, i think beams should also have the ability to target engines with their good accuracy, so that any remaining ships after a battle get a debuff to movement and maybe even give you sight of them while their engines are giving off smoke and making them very visible until the engines are repaired, making it a good defensive boost to offset the kinetic offensive boost. i think these changes would help make both weapon types more fun for people depending on their tactics like missiles has done with it's ranged ability.