Having owned both, I would say that an M Coupe is every bit as impractical as an S2k in terms of everyday driving. I am comparing 99M to 00S.

Traffic: The M clutch is heavy and the engagement is abrupt, making it a nightmare in traffic. Also gets hot, quickly. Score 1 for the S.
Utility: The trunk area is oddly shaped and it's easier to fit a set of golf clubs in the S. On the other hand, I think the wagon style of the M gave it some flexibility. The M will allow you to take a small dog and a passenger. Call this even.
Highway: As firm as the suspension is in the S, I think the M coupe is even stiffer. Cabin noise is slightly less at highway speeds in the M. So for highway comfort, call it even again.
Comfort: The M does have slightly better seats and far better stereo (doesn't take much to beat the S there). The AC is better in the S, but both cars get hot in traffic. Edge to M.

I think if you need to drive one for a day, the M coupe would be the one. Really feel like an S drives like any rwd car. The M Coupe is a wilder beast than an M3. Must be due to the weight distribution and driver position. It takes a long time to get used to.

If you want a convertible, why isn't this a M Roadster vs S2000 question? M Roadsters are easier to find. There were only 400 or so of M Coupes with the 315hp engine in the US. A full country search of autotrader only turns up 20 or so M Coupes of any kind.

All this said, if you're really serious about buying and your credit checks out, you could probably talk a dealer into letting you take an S2k home. He will probably put some limit on the mileage, and you should both walk over the car and mark every little imperfection.