I feel the Apex is a lot more versatile. With the Apex you can use a left or right hook shot, drop shot, normal shot, plus different levels of backspin. With the Flatline you are stuck with just the pre-set backspin. Another plus to the Apex is if you get a different gun, you can just swap the barrel out and still use it.
Shot wise they shoot the same distance with the Apex at the maximum backspin setting. With the Apex you have to tilt the gun up some because of how it uses a ramp that angles the paintball down as it exits the barrel to create the spin. With the flatline you will be aiming a bit straighter down the barrel if that makes sense.