The most memorable scene in Independence Day is almost certainly when the alien ships deploy their city destroying ray for the first time. It was jaw dropping how unexpectedly quick three of Americas most prominent cities were annihilated. When I think back to the first time (of several) that I saw Independence Day in theaters, that scene never ceased to amaze and excite me. I imagine most of the audience felt the same way.
But outside of that, the alien weapons in the first film were rather conventional. Force fields? Seen them before. Mini ships to dogfight with our airplanes? Not that original. In the sequel, the invaders need to have some new tricks up their sleeves. Some new form of weaponry or attack method that will inspire that same jaw dropping awe. They should, of course, keep the death ray; it wouldnt be Independence Day without at least one of those being fired. But give the aliens some new toys to shock and surprise us along with their familiar arsenal.