Horses for courses really. I didn't want to mess about with the engine cover so I went for the Carbonio intake with ITG panel filter. If you really want a CAI then you have to resign yourself to the fact that if you want to revert, or sell the car standard you will need a new engine cover.
Although there isn't a shortage of Mk5 bits around so I doubt a used one would be hard to find when the day comes.