Firstly, Mario 3 does not have better platforming than Rondo. Different platforming (inertial), but not better.
No, better. More varied, more fluid, more agile, more responsive, more creative. The platforming in Rondo is simply average, nothing remarkable at all, nothing to offer anyone that can't be had elsewhere and better. Being different doesn't save it, as being different doesn't save Zelda 2 from being inferior in side-scrolling combat to Rondo, according to you. Which I wholeheartedly disagree with, for reasons Siobhan pointed out
Second you need to compare moment to moment gameplay in broad strokes. There's a reason I divided things into action and puzzle instead of platforming and spell casting.
The point is moment to moment, Zeldas (and Okami for that matter), don't have anything going.
All the other games you mentioned do. The only exceptions to this with Zelda are some of the minigames (and how much of the 10 or so hours it takes to run a Zelda are spent there?), which incidentally betrays the entire design of Zelda's moment to moment gameplay. That is, complete modality. Everything is a minigame "now you are solving a sokoban puzzle" or "now you are fighting 2 lizalfos" is no different to "now you are shooting baloons from a horse".
Ys and Rondo do? Those games are comprised of tons of trivial encounters, without any of the other elements LoZ offers. Now Volgar the Viking, that's a game that where nearly every moment is significant. Every enemy or hazard placed in that game is a viable threat to your progress. Still doesn't replace the LoZ experience. And fighting enemies is fighting enemies, like it is in any other game. It may be simple, which there is nothing wrong with, but it's a core feature, not a minigame.
What makes Zelda Zelda is that all of these are linked together by "Adventure" i.e. walking simulation and conversation simulation. If you don't care much for this, then you are better served elsewhere for the other bits.
As it turns out, Zelda fans do care for the whole package. Not "bits", which is an autistic way to judge any piece of design. They are not mechanicsfags attracted to one feature executed at the highest level. Ys Origin is not any kind of adequate replacement or upgrade for the Zelda feature-set, nor vice versa. Do we need to enumerate the ways they are not? Their developers are not even attempting to present the same kind of experience. Even less so Rondo of Blood, which is a merely a stage by stage combat gauntlet, essentially an arcade game, not a game whose legacy is both from the arcades and open world RPGs. Certainly not any of those puzzle games.
There is no walking simulation here. There is no attempt to replicate the experience of walking, no evidence the developers intended this. Are you being cheeky? Are you saying this because there isn't a trivial encounter every 5 steps like in the Ys games? What, if anything, is being simulated* is the hero fantasy journey, of which travel of some sort is always present.
*Well most accurately, from the horse's mouth, LoZ is a simulation of exploration in the Japanese countryside during youth.