THye couldn't put the Voyager level Voth in the game. That tech was broken as heck.
They can. Imagine guerilla warfare in space, or stealth missions. They just can't put in missions that allow you specifically to pew pew the Voth in a straight up fight(not without the help from allied Voth anyways). This, of course, would require Cryptic to create different gameplay mechanics other than kill everything in sight.