It's a very different car. Thats like comparing an SUV to a minivan when all you are looking at is the 3rd row seats. They both do the job but have a lot of differences. Depends on what you want really. I think the FR-S is a great looking car and is RWD as well. The Si makes a great all around car and is pretty capable even in inclement weather, with proper tires, and yes, Im sure the FR-S with snow tires is fine too.
Overall I think the Si has the potential to be a better "everyday" car that you could take to the track simply because of the Sedan option. A 4-door car is a lot more practical for a lot of people. I'm a bit biased, this is a Honda forum, but I vote for the Si.
I think the FR-S is a lot sportier looking and the RWD is a big plus. Around the track I think the FR-S would probably be slightly better because of that. However, there are a lot of really fast auto-x guys and track guys driving Civics. People do say the FR-S is really really fun to drive, but if you can only have one car then maybe a 4-door Civic Si is a more useful car. Besides no one ever expects a sedan to be fast.
EDIT: I also don't want to drive a Scion. Maybe a BRZ cause it's a Subaru. Just a bit more upscale. Also there is a difference in handling between the two. Something about the spring rates being different and the FR-S being a bit more tail happy than the BRZ. Not like anyone is going to leave the suspension on either alone though!