1. I have not found a filter which does not add additional flare to my lenses - be it cheap kit lenses or be it Canon L lenses. For this reason I do not use filters unless needed (i.e. polarising filter).
I have B+W MRC UV filters on all my lenses. As some have stated, a filter is required to complete the weather sealing on most L-lenses. Besides the debateable 'protection' argument, the B+W MRC filters are more smudge resistant and easier to clean than the front element of most lenses (Canon has started applying a fluorine coating to the front and rear elements of their newest L lenses, to make them more smudge resistant and easier to clean).
I don't think that a high quality filter adds significant additional flare to a lens. Since I am reluctant to make a claim like that without empirical evidence, below are some comparison shots (click for larger images). I used a 5DII and two different lenses (a 70-200mm f/2.8L IS II @ 200mm, since that's the subject of this thread, and a 24-105mm f/4L IS @ 24mm), each shot wide open and at f/11 without and with a B+W MRC UV filter. The appropraite lens hood was used. Light source was a halogen lamp (150W equivalent) in the upper left corner of the frame, in an otherwise completely dark room (literally, a darkroom). This is something of a worst-case scenario - a small, very bright light source, a black background, and no extraneous features in the image to mask the flare.
70-200mm f/2.8L IS II @ 200mm:
24-105mm f/4L IS @ 24mm: