Faster in a straight-line race: MS3
Faster around a track: RX-8
Even though I'm not that fond of the body style of the MS3 (was really hoping for a sedan when they came out) I would be happier without all the quirks the RX-8 brings to the table. I'm sure there are plenty of success stories that remain untold, but the horror stories I've read about that car are more than enough to keep me from even looking at one. IMO, I don't think an RX-8 is happy being a commuter or grocery getter. It wants to be on a track having the crap revved out of it, eating apexes for lunch. The kind of driving it will see in an average day puttering around town is actually worse for the engine than a track day.
If you want a great-handling, reasonably powerful car that can transport 4 people in a pinch, and you don't mind winding an engine to 8K to get any real power out of it, get the 8.
The MS3, IMO is far more user friendly and quite a kick to drive. Room for 4, or 5 if you're desperate or a whole lot of 'stuff' with the seats folded down. Show it love with premium unleaded and use good quality fluids and it'll love you back.
It really depends on what you need a car to do for you.