I’ve commented on this in another thread — perhaps with you? — and I agree that the odd position of the shift lever has something to do with it (if you feel under the boot, it bends something like 30° at about the point where it passes through the console).
But it grows on you, or at least it did for me. I’ve had my 2011 Express for a year and a half now, and while I’ll never equate it with the Mazda that I traded in, I’m long past the point where going through the gates is, well, automatic. If the clutch lasts anywhere near the Mazda (165.000 miles on the original, and only just beginning to show signs of slippage on hills), I’ll be well content.