My issue with the controller isn't the L trigger/joystick issue, as I'm not aware of any games where those two things would ever be used at once (L is meant for use in Dpad games). The issue for me is the fact it's basically just an Xbox joystick with a gate around it. While the gate is most certainly welcome for steering in games like Waverace or F-Zero where those grooves help you keep in line, the general feel and looseness of the stick just doesn't feel right.
Call me crazy, but there's a lot of range with an N64's joystick, and a lot of resistance, enabling more fine movements. I don't feel like I'm able to control anything half as well with this thing.
I do agree the original controller's layout is terrible now. It was amazing when I was a kid, but the controller doesn't really seem to fit my hands well as an adult. The Hori pad, at this point, is still the best option in my opinion. Better joystick than this by far, and a better layout than the original. Just wish the Hori pad wasn't so tiny.