I don't think that 3 way vs. 2 way has much to do with it. I suspect that the Yamahas are more sensitive, which gives them greater volume at a given volume setting. Also, the M3s may not put out as much bass, as you said, because they're 6 inchers, as opposed to 8s. I imagine that the cabinet is smaller, too. Do you have any adjustments made to the tone controls "left over" from the Yamahas? I would suggest you put the tone controls to neutral (and turn them off entirely, if possible with your receiver). This could make a big difference. Now, I've only heard the M22s, but I was blown away by them. I'm considering the M3s or the M40s or 50s for various reasons, but I've not heard them yet. I'd also play with positioning a bit.
BTW, the M3s (& 40s and 50s) are considered (or used to be, at least) to be on the warmer side of Axiom's lineup; in other words, they're not accused of being bright as often as the 2s, 22s, 60s, and 80s.
