But variations on it were done on Star Trek (the virus part, not the Apple part) several times, ranging from TOS right through Voyager. Don't think they'd done that one on Enterprise yet, but they were cut off before they could get around the recycling that particular plot point.
I do think I have a way to fix this "stupid and impossible" plot hole in Independance Day, however. I've always wanted to cut in 15 to 30 seconds of the existing footage of the back of Brent Spiner's head talking to Jeff Goldblum and substitute a little of my own dialog to the scene where he's explaining how they have had this alien spacecraft for years, but haven't been able to do much with it till this new fleet arrived. He could simply add a statement that the only thing they've accompoished in all those years is to figure out how to easily interface our computers to theirs. POP. Plot hole gone.
See how easy, problem solved! They need to hire you for "fixer-of-plot-holes". Could be a whole new career for you.