Key points:
-NiGHTS research and Development began immediately following Sonic and Knuckles completion.
-About 6 months in (around early summer of 1995), they realized they needed analog controls for the game to play well, so they started developing the 3D Controller.
-They went through about 100 designs
-There's absolutely no mention of the N64's controller.
So the basic fact is the Nintendo 64 had no influence on Sega's decision to create an Analog controller. They were working on it before Nintendo even revealed their analog controller.
Sega simply didn't package it with the system because they already had stock without it that wasn't selling. Sony later did package there analog controller with the PS1, but their system was actually selling so they had no stock to actually produce. If the Saturn was selling well, you can bet your ass they would have bundled it with the system. Sega did however bundle it with the flagship game they wanted to show it off with. So really that's showing just about as much faith in it as Nintendo showed with the N64.
And here's the source for why Nintendo delayed the N64:
http://www.nytimes.com/1995/05/06/bu...me-player.html