I have problem when a mod actually makes a machine less fun or harder to play. For instance; bright LEDs in the backbox that cause a ton of extra glare on the PF glass, LEDs strobing that make the balls harder to follow, mods/toys that block the view of the ball, etc.
What really bothers me are games that people have taken a lot of time and money to bling out, yet it still has old black rubber, flippers that need rebuilding, dead switches, needs leveling, etc. To use the car example, this is the car will all kinds of ground effects and wings but needs paint and has dents/rust or a car that has a huge stereo that does nothing but rattle due to no soundproofing so it sounds like shit anyway.