Star Trek class warships are more mobile and their shields render them completely impervious to fighter craft like a Tie Fighter with small power blaster cannons.  The photon torpedo allows the Star Trek vessel to pound a star destroyer from greater range and can be targeted in pre selected firing sequences for more accurate strikes.  The super star destroyer is huge and carries planetary assault assets such as imperial walkers and legions of storm troopers, but is susceptible to fighters as was proven in Return of the Jedi.  Once the shield towers are knocked out, the super star destroyer is a sitting duck.  Furthermore, a Sovereign class starship can fire from any direction with concentrated spreads whereas a star destroyer must maneuver in close for a side swipe where most of its cannons are located.  All a Federation battlecruiser would have to do is get behind the star destroyer where it cannot fire concentrated bursts, and it's all over but the crying. 😀