Have you driven them both? I have, and I bought the Evo. They were really no comparison. I've always been a sports car guy (I've have owned a few Miatas, an MR-2 Turbo, a few 911s, a Boxster, an M Coupe, etc.) and I've never really liked turbos or AWD cars before, but the Evo is a bellweather car. It is just such a great driver's car. I couldn't believe how much fun it was. You'd be driving along and catch a glipse back and realize that you're in a sedan - it was weird.
I loved my Evo and only sold it because the budget was tight when the Elise came in a few months early. I will buy one again. Hell, my wife even want's one.
If you haven't driven them, I reccomend that you do. That's the only way to make up your mind, and it will be a lot of fun.
P.S. I like the S2000, but it really doesn't seem like it should cost as much as the Evo, especially the MR.