Sad to say this, but I would go with the civic. My dad works for GM and we own all Chevrolets, but from personal experience I would stay away from GM cars, at least the economy cars(i know the SS is a higher up trim, but still the stripped down cobalt is an economy car, lots of same parts.). Dont get me wrong, I love GM's trucks, I drive one myself, and I wouldent trade it anyday for a ford, dodge, toyota, nissan, honda, or whatever trucks out there on the market, except the Chevy Silverado SS lol.
As for a Civic si, they are good cars, honda has a good warranty, and as for which car is faster or not, it all really depends on what you do with it in the end. Account for the fact that the Cobalt has a SC, even though its a stock GM SC, its still there, so add one of equal performance to the SI and I would feel confident the SI could take it. But since I really doubt any performance company would produce an aftermarket SC that crappy, you'd have to go with a bigger, better one, or a turbo >=D!
Anyways, yea, SI has my vote between those two cars.. I'd still say go with a truck, I can at least climb a curb, lol.
If you do end up with the civic like you say you are likely to, do what most people do to any car first.. Exhaust, intake, and tune.
For the exhaust, get a nice header, catback, test pipes, and a cutout if you plan on racing. Cutouts may sound obnoxious on anything with less than 5 cylinders, but they arent expensive and can really see some nice gains in HP/TQ. They even make electric cutouts so you can open/close with the flip of a switch which is useful for cars because you cant always reach under and turn those wingnuts without a jack lol.
-Lurius