My best friends are all part of the Cavalier/Cobalt crowd, and I cannot agree more that those two cars are about 10 years behind the times in terms of fit/finish.
But, a stock Ecotec can handle about 300 whp (I've seen it). A stock Ecotec is the 2.2L, naturally aspirated version of GM's global 4 cylinder, which the LSJ and LNF are built off of (which power the Cobalt SS and Solstice GXP, respectively).
Ive seen Cobalts with nothing more than a Stage 2 upgrade put down 221 hp at the front wheels on a Mustang dyno. Now, lets assume the new engine is 260 hp, and comes with a Stage 2 upgrade. That will already put the Cobalt close to the 300 crank hp mark. That is where Chevy will win out over the MS3 becuase of their Factory Backed Staged upgrades which can increase power well past 300 hp, all with a warranty. So, already, the engine is better built than an MZR and is more mod-friendly.
I also look to the gearing. The MS3 does not need a 6 speed with so much torque on hand. If you were able to hold power to redline, a 5 speed would be the best choice. This is where the Cobalt SS may shine also because even with less displacement, Chevy has a way of tuning for nice flat torque curves.
If you are looking for an all around car, the MS3 is the winner. But if you want a straight-line performer, I might have to put money on the [future] Cobalt SS. But, that also depends on the driver.