http://www.stardestroyer.net/tlc/Ion/index.html
An ion cannon works by overloading relays. It sends massive amounts of ionized energy throughout the hull and the computer system, in effect, 'shorting it out' until the ions disperse. We see Trek ships getting 'overloaded relays' in nearly every episode..so ion cannons would have a hay-day. And ion cannons are far from useless against shielded targets. They stick on the shielding for a fraction of a second before penetrating completely.
This would take care of any Starfleet Shields.
Empire ships use "Turbolaser", which is much more powerful than standard lasers.
That's right. We have pleanty of evidene on screen that Wars weaponry is far, far more powerful then anything Trek can hand out. And what Trek can hand out wouldn't do a whole lot.
A) You have partical sheilding that obsorbs kenetic energy, ray shielding that does the same to energy weapons (IE, a phaser blast, or an explosion from a photon torpedo.)

Wars has ion cannons..'nuf said.
C) Wars has massive ammounts of fighters. A Trek ship could only pick them off one at a time..
D) Capital-scale turrets that are deisnged to track fighters..would have absolutely no problem tracking a Trek vessel.