I think unless you need the 4 seats, you`d be better off with the S2k. couple of reasons:
S2000 IMO is designed with less compromise and more as a racing car than the FR-S: double wishbone all the way around, engine sitting aft the front suspension completely. I see the FR-S being a VERY capable car but it still addresses the daily practical problems such as the rear seats and cupholders

S2000 doesnt care for all that.
However, I`m never relaxed in a S2000 like I am in a miata. I want to say it's the power difference, but I dont think that's the only reason why. I feel like S2000 is more snappy and quite difficult to drive fast (or I`m just a bad driver LOL) but I get the weird feeling that the FR-S will be able to driven easier at the limit than the S2000. But then again that is all just a speculation since none of us has driven it yet.
and if you prefer the way the FR-S looks over the S2000, why not?