It really depends on what you want and like. The MS3 and MS6 are focused on different target markets. The MS6 is a relative bargain, considering you can get one for the same price as a MS3 (I envy you guys in the US), but it's only a bargain if it meets your needs.
MS6:
4 door sedan, fairly subtle styling - portrays more "mature" image, physcially larger with more elbow room inside, more GT oriented.
AWD for consistent performance in varying weather conditions.
Heavier and ultimately less dynamically responsive (unless you mod the susp). Also, more complex (AWD system).
MS3:
Sport compact, younger "sportier" image implying so-called "active lifestyle", not as much elbow room inside but considered not as much an issue as "younger" customer base tends to be "slimmer".
Hatchback/wagon body to complement "active lifestyle".
FWD because that's what most of the other cars in this segment are (GTI, Civic SI, Cobalt SS, Caliber SRT4, Saturn Ion Redline), and to keep the price down.
Lighter and dynamically more responsive, but ultimately gives up some performance due to better traction of MS6 AWD.
Look at the Subaru WRX (not STI) and Legacy GT as examples. Both share the same engine and basic drivetrain, both are similarly priced (at least they are in Canada), yet they're focused on very different markets.
For me, it came down to the conditions I drive in. Being in the Pacific Northwest the pavement is wet almost 6 months of the year. Having AWD means I can extract 95% or more of the car's performance year round, while with FWD I'd just be spinning my front tires 6 months of the year. My last two cars have been FWD and I got so frustrated with not going anywhere when the light turned green that I swore my next car absolutely had to have AWD. I'm also older, and having the extra room sure helps, especially after 21 years of raising kids that can't sit still.
If you live in California or somewhere where it only rains a few weeks a year, the AWD is probably not a big deal. Do you do like to do lots of quick standing start acceleration (ie. stop lights), or do you prefer immense passing power once you're already moving? If you like quick acceleration from a standing start in all weather conditions, get the MS6. If you drive mainly on country roads in warm climates and you don't stop frequently, get the MS3, because it will be quicker in roll on acceleration since it's lighter and traction isn't as big an issue as you're already moving. Do you absolutey have to have the utility of the wagon body? Etc, etc.
Figure out what your priorities are and see which car fits the best.