What I personally do is, for the purposes of how Starfleet views their ships and weapon power, ignore penetration ratings in favor of offensive ratings when you're placing systems.
In Starfleet's eyes, pulse phasers are clearly better because of their power (offense) to mass (space) ratio, since they aren't bound by the game mechanic of total weapon penetration.
Davy Jones
"Frightened? My dear, you are looking at a man who has laughed in the face of death, sneered at doom, and chuckled at catastrophe! I was petrified."
-- The Wizard of Oz