Having your breather pipe connected to your inlet tract provides a vacuum, this vacuum draws the gases from the crank case making it the most efficient setup to reduce crank case pressure. A decent baffled catch can should be CATCHING the oil vapour as it passes through the can whilst the air continues to the inlet. These gases may not be fresh clean air but if your running a cold air intake this will completely overwhelm the amount of air coming from the can, and dilute it so much with clean air it will not make a difference.
The vacuum is the reason why ALL engines are plumbed this way from the factory, it's simply the most effective way to reduce crank case pressure.
As soon as you add a filter(a way for air to enter or exit) the vacuum is lost.
