I've had similar thoughts to this at times, but I'm not sure that it's true.
NES: Nintendo really pushed the boundaries of 8-bit development here. SMB3 did some some pretty awesome stuff. Games like Zelda and Metroid also pushed what a game could be. Other games like FF3 and late comers like TMNT2 and Battletoads may have been the absolute max of the system, but many Nintendo games really broke new ground.
SNES: On launch it was definitely non-Nintendo titles that looked the most impressive. Castlevania 4 and FFIV stood out as next-gen much more than SMW - although F-Zero was also very breath-taking, as was Pilotwings. In the end Rare's DKC series was the presentation benchmark. So if you want to count Rare as Nintendo, then I think they really pushed the system's abilities.
N64: For me the groundbreaking games on the system are M64, OoT and MM. So I would say that Nintendo really pushed the N64 and were at the cutting edge of game tech during these years. You could also include Goldeneye for being groundbreaking.
GC: I would call Zelda:WW the benchmark.
Wii: SMG and Xenoblade were the games that pushed the system the best.
Wii U: To date, the best presentation is SM3DW.
In summary, I think that Nintendo actually does push the limits of its hardware. I think lately they are really missing the skill of good third party support that can make games with different themes and presentation that can push the system, but overall Nintendo has frequently made some pretty ground-breaking titles. Even if sometimes they were exceeded at some point by a 3rd party game, it's not necessarily for the better. A game like Doom on SNES may push the system beyond its limits, but I don't really think that's a good thing. Programming within the limits can give you a better result, and sometimes takes more true skill.
Nintendo has often pushed their own systems tech - I'd like to see that a little more with Wii U. Mario and Zelda games should really be ground breaking. I'm hoping for something good with Zelda U.
