I like the way the 6 drives better.
There's a buzzy feel to the way the 6 goes down the road (on the right wheel and tire choice, mind), and the steering on the first generation Mazda6 is much better than the steering on the first generation Mazda3. The best thing you could say about the Mazda6 is that it feels like a bigger Protege. The Mazda3, despite being better than the Protege in every other way... doesn't. I may be going out on a limb here, but I've always felt the 3 was a bit anti-septic compared to the Protege and the Mazda6.
The thing is, the Mazda6 is incredibly light for a modern mid-sizer. And it's incredibly well-balanced. The Mazda3, on the other hand, is porkier than the Protege was... though not as porky as its platform-mate, the Mark II Focus. So you have a light car with a suspension built to handle big loads versus a heavy car with a suspension built to handle light loads... whaddaya get? A sporty 6 and a floaty 3.
I guess if you got the 2.3 hatchback in sport trim, it'd be as nice to drive as a 6 (probably better), but we didn't get that here...
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How much do I like the Mazda6? I'm borrowing my third one for a magazine review next month. Which I timed to coincide with a track-day.
Which, God-damnit, didn't push through. Now I've got to find an excuse to go attacking a mountainside sometime in that week, or the borrow will be wasted.