There is no reason not to replace the regulator in a new design with a different regulator capable of supplying more current.
However, there is more to making a 3A power supply than simply using a a regulator chip rated for 3A. The chip you mention is still a linear regulator, and is not any more efficient than the normal regulator chip. That means that if you want 3A out of it, it will end up dissipating (Vin - 5) * 3 Watts of power. For the "normal" input of about 9V, this is 12W of heat. The fact that the 323 is rated for 3A (and 30W) means that it IS capable of dissipating that much heat, but you WILL need a substantial heat sink, and it will get warm. (such regulators tend to have built-in over-temp protection, so if you build it wrong, it'll just turn itself off. Maybe.)
IMNSHO, if you want more than the 500mA or so that the normal arduino regulator provides, you should start looking at switching regulators for their greater efficiency. You can design your board for an external 5V regulated switching power supply like http://www.bgmicro.com/index.asp?PageAction=VIEWPROD&ProdID=12673, and you can avoid all sorts of issues...