Well, have yet to play SotN but if Circle of the Moon is anything to go by, then yeh, Hollow Knight is leaps and bounds better.
Before playing Hollow Knight I was replaying AM2R and thought to myself "man, this fan game has some of my favorite Metroid boss fights actually, not bad!" Then I get to the more or less 3rd boss fight of Hollow Knight, the Mantis Lords, and it easily blows everything from Metroid out of the water. Really, the entire combat in Metroid games is hella bland in comparison to what HK has to offer.
Hollow Knight has it all, really. Gameplay, game design, quanity of content, quality of content, art direction, animation quality, soundtrack, lore, and story.
For as good as the atmosphere is in e.g. Metroid, S. Metroid and Metroid Fusion, there's very little interesting story told actually. Compared to that Hollow Knight creates an interesting world and tells a good and fairly concise story, which I didn't expect hearing all those "basically up to interpretation" remarks. Not that there isn't some of that but the main events concerning this 'Vessel' storyline are clear (and interesting). Beats hearing a bit more about Chozo any day of the week.
For all the complaints about having a Geo currency, I see little about comparing neat gameplay altering charms that can be combined in many ways to fucking '+5 missiles' upgrades! Oh boy, I've increased my maximum missle count from 105 to 110, what a joy. Let's see what my Energy Tanks, S. Missles and S. Bombs are at zzZzzzZz.