In some ways, it's hard to say. The Civic Si can be configured with a nav unit, and has a generally better audio setup than avalible in any other Civic trim. I think since the last Civic Si was discontinued, it's more of a "top level Civic with MT," rather than "a slice of something different," anymore.
Just my opinion.
But as others have said, "apples to oranges." They are not really directly comparible, but I am cross shopping between the two, right now. Civic Si sedan w/ Navi vs Impreza Premium MT. It's a tough decision, for me. I'm still holding out for the 2013 Civic before taking the final step. The Accord sedan was on the list, but you cannot configure the MT models in any meaningful way, though it gets decent fuel economy for a large "midsize" sedan. If the 2013 Civic Si gets that engine (not likely), it will cement the choice. Otherwise, there are several other considerations to make; the Impreza has only 5 speeds; the Civic requires premium (93); the Impreza has 4WD; the Civic gets a mechanical (not viscous) LSD!; the Impreza is more expensive; the Civic Si seems to get ridiculous insurance quotes in my area.
EDIT: I said more expensive, that's in my area (Sactown), for whatever reason, it just is. Of course, negoatiations may vary, especially if the 2013 Civic proves a hit and doesn't get anywhere near the discounts of the 2012 Civic.