Yes the N64 pad had spacing issues and the analog stick should have been on the left hand side. It was a very off putting design. My hands cramp whenever I use one so it's not as comfortable as it should have been.

Reach "all the way up" to hit Z?  It fits directly under your index finger.  OoT was a blast on the N64.

The N64 controller actually had a more accurate analog stick than any of its successors, the main problem with it is that it would wear out quickly (especially thanks to rotating it quickly to kill Bowser in SM64).

^And don't make me start on Mario Party eh!

God yea Entroper, my N64 controllers lost their analog sensitivity making them hard to play with.

The worst would be the N64. Second would go to the Xbox and the 360. I actually liked the Jaguar controller as there were a ton of options. Keeping all the add-ins was annoying though. The best though are the Playstation ones.......all of them are the same really. They are the most confortable, and the buttons are all in the right spots. No hunting or adjusting.

 Wait...my memory is a little foggy. 

 There wasn't a Z button under the third prong, was there? If so that would be better and make sense.

 If there wasn't, then I cannot possibly see how it would be under your index finger, unless you had gigantic hands.

The Z button was under the middle prong, right behind the analog stick.

 Ah, alright, that makes a lot more sense. I sold my N64 long ago.

What was the point of the left side of the controller? Nintendo could have cut it off and the controller would have been the same for like every game.

I used the D-pad for menus, and they were sometimes used for uncommon commands.