I am a huge Ys fan and would vote for Book I & II in most scenarios, but SMB3 was such a monumental, groundbreaking game that it's really tough to justify voting for what's essentially a beefed up, several-years-old port of Ys: The Vanished Omens (and the mazey and sometimes tedious Book II). SMB3 is iconic, pushed the NES to its limits and is filled with character, exploration, secrets and creativity. Don't worry though, I didn't vote. 
You've done a good of accurately describing what you think of the games, just not the games themselves. 
If you reversed your descriptions, it would be much more accurate.
I realize it is an uphill battle debating this on a Turbografx forum, and let me preface this by saying I'm platform agnostic - I grew up loving SEGA but still had Nintendo, Apple, Sony and NEC systems growing up and respect that each system had diverse and solid libraries. The facts remain (and they were mostly facts, not my thoughts on the games), that Ys is a port of two older games (maybe a battle against Super Mario All-Stars would be more fitting?), and other than the awesome CD-tunes one that didn't particularly push the envelope of the TG from a hardware perspective. Nintendo packed additional chips and hardware inside SMB3 to allow it to accomplish split-screen scrolling, animated tiles and hardware feats that hadn't all been brought together in such a complete package as this before. From a software side, SMB3 pushed concepts like non-linearity, overworld interfaces, secret hunting and sandboxing. Being able to fly in that game allowed players to explore each level in multiple heights and directions that surely inspired concepts from other classic games like Dragon's Curse or Sonic the Hedgehog. The physics of the game helped popularize the found art of speedruns and the secrets and clever level design encouraged players to interact with games in a new kind of way - you could replay levels and just try different things, finding pipes in the sky, warp flutes or even a secret to play on an entirely different plane. Even ignoring the multiple ways you could play or finish the 90 different levels, you could also spend time with various puzzle and matching games, versus games or even an included version of Mario Bros. Before Shenmue or GTA it really was one of the first sandbox kind of games. Just look at the response to Super Mario Maker today to see its fundamental influence on the creativity and the imagination of gamers all these years later.
The other thing that I think really makes SMB3 standout is that it still stands the test of time. There are better Ys games (and even better ports of Ys Book I & II) available today (Oath in Felghana, Seven, take your pick), but the physics, variety and creativity in SMB3 peaked in 3 - it's still to this day cited by many (most?) as the best Mario game.
Ys Book I & II has simple gameplay and a predictable structure - you run into shit and then go into a town and talk to people. The production values on the TG are great and I love the amount of NPCs and dialogue you get to experience, but it's still by comparison a much simpler and basic gameplay experience. What did it pioneer that Zelda hadn't already a few years prior? I'd argue as the series evolved it had greater attention to strategy and the complexity of it's awe-inspiring boss battles, but the game in question here is quaint by comparison. I just don't see how the TG-CD port somehow stands up today one of the best games ever made, but I'd love to hear why.
What about SMB3 is groundbreaking? It's more of a well polished collection of ideas and mechanics found elsewhere, kinda like Apple hardware.
Was the iPhone groundbreaking? The Macintosh? I'd argue yes, because they changed the way we interacted with technology. Others had tried those markets before, but the secret is putting it all together and making it an experience so refined it incites a paradigm shift. SMB3 did that to platformers and game design in general.
