I have been thinking about this quite a bit lately, and I actually think it has far more to do with the shape of the DualShock than the position of the sticks.
If you really stop and think about it, this makes perfect sense. The DualShock controller was never designed to have analog sticks in the first place. The original PS controller was designed to be held with one thumb on the D-pad, and one thumb on the face buttons. Putting the sticks on the controller was more of a bandaid than anything, and Sony didn't change the shape of the controller at all when they added them.
The problem this presents is that when you reach your thumbs to the analog sticks your palms are not holding the controller the way it was meant to be held, and this creates discomfort. If the position of the sticks was the issue, then you should be able to recreate the discomfort when holding the X360 controller with one thumb on the D-pad, and on thumb on the right analog stick. However, the controller is still rather comfortable when you hold it in this position, much more so than the DualShock. This is because the X360 controller was designed with all of the inputs in mind. The shape of the controller was meant to accommodate holding it with your thumbs in all manner of positions. The shape of the controller is such that it is equally comfortable to use the D-pad as it is to use the left analog stick, and the same could be said for the right analog stick, and the face buttons.
Here is another example to consider. If the placement of the analog sticks was the root of the problem, then that discomfort should be remedied by holding the controller as if the left analog stick is where the D-pad is currently. What happens though is that while the placement of your left thumb is where you think it should be, the controller is still relatively uncomfortable when using the right stick in it's current position.
We can look then at the overall redesign of the DS4, and it's longer/wider shape should accommodate the controller being held in all manner of ways, just as the X360 controller is. I am actually of the opinion that people are going to find the placement of the sticks to be better for FPS's than the XB1 controller once the shape of the controller is such that holding it in such a way is viable combined with the improved sticks. Using the sticks in tandem should become easier when both of your thumbs are in the same position. It will be a subtle thing, but over time I think people will notice it to be a little more usable. I think of it along the lines of patting your head and rubbing your belly. If your thumbs are in the same position, then your brain has an easier time processing the movement. You can experience this for yourself in an exaggerated way by holding your hands out in front of you and waving them in circles. It is easier to do when both hands are at the same level than it is if the are off center. Again, it is subtle when using a controller with your hands close together, and only your thumbs being manipulated, but it does make a difference.
Likewise, I think that the XB1 controller will likely continue to be more comfortable in games where you primarily use the left stick and face buttons in tandem. Your thumbs being at the same level just feels more natural.