Never! In what parallel universe?
The Megadrive didn't even have a 6-button controller as standard for years - if it ever became standard actually.
The AX-1E, for the Megadrive:
http://en.wikipedia.org/wiki/AX-1E
http://homepage.ntlworld.com/denise.thorpe1/ax-1e.jpg
Six years before the N64!
Btw, analog triggers is merely a marginal evolution of Nintendo innovation with the SNES pad.
The AX-1E was out the same year as the SNES (maybe even before it?) and sure as hell isn't based on the SNES pad!
The AX-1E layout appears to be based around stick (left thumb), throttle (right thumb) and rudder / weapons (left and right variable triggers). Little surprise the first game it worked with was After Burner 2. It owes nothing to the SNES and everything to remote control devices for things like planes and cars.
It wasn't standard either, and only ever worked with a handful of titles. Unlike with N64, where every game could take advantage of precise analog controls...
The Saturn "3D controller" as it was called, actually worked with every Saturn game, but only a few in analogue mode. In analogue mode the D-pad could still be used. N64 did have analogue thumbstick as standard, but someone else coming up with analogue thumbsticks years earlier takes some of the shine off it!
It may be your opinion it was appalling; IMO the only truly appalling thing about the N64 pad was the D-pad, which was very poor. All it was good for was to act as auxiliary face buttons. The pad was also too large, although that came as a large part from the three-prong design...
I think Nintendo must have thought the pad layout was appalling too, in retrospect. It was their first go though, and at least they made analogue a standard thing and advanced the movement for everyone. The actual analogue stick on the N64 was actually very good IMO, and one of my favourites.
To call it "Sega Saturn's layout" is just bullshit, as it's the standard NES layout but with the D-pad replaced with the thumbstick. Give credit where it's truly due!
Nintendo tried to make an analogue pad and they came up with a trident (wtf!?), digital triggers and a truly horrible "C" button. They didn't know what to do with the Dpad and stuck it on an extra prong out to the side where you couldn't even reach it. It's crap! It's so crap that Nintendo dropped the ENTIRE LAYOUT along with the god awful "C" button and didn't make any reference to the design, at all, in any of their future pads ever again.
Sega made an analogue pad and put the analogue stick top left, the Dpad underneath and inset so you could reach it without repositioning your hand, and put analogue triggers on the top.
Hmm, I wonder, which does the GC pad base its layout on; the N64, the NES, or the Saturn/DC? Even Miyamoto joked about how the GC pad looked like the DC pad. Based on the NES pad? Not in any but the most general sense.
Sony OTOH actually did based their pad on a Nintendo layout and it shows very, very clearly; the Dual Shock is a SNES pad with analogue sticks stuck on the bottom. The GC pad was completely different and almost identical to Sega's designs rather than any of Nintendo's previous ones.
You're serious? The Megadrive pad had a large button in the center with three bean-shaped buttons surrounding it? Gosh, I never knew!!! All this time I thought the Megadrive pad was three buttons in a slightly arcing row!
(2 rows with the updated streetfighter-compatible pad.)
Look at the buttons and how you reach them. Three buttons in a row, angled at about 30 degrees to the line of the pad, with another button perpendicular to and above the middle button. You might claim that Nintendo had never ever seen a Megadrive pad, and for the sake of argument we can accept that for now, but the idea behind the optimal layout for the four buttons is the same.
Maybe it's just another thing that Nintendo independently re-invented, having failed to notice one of their main competitors doing in their most successful ever product.
Nintendo made the right call IMO; the Megadrive / Gamecube arrangement of face buttons is better than the diamond layout which everyone (including Sega) ended up copying simply because Nintendo made it popular.
I don't agree.
But 1990 comes before 1996!