It's a tough choice which requires an explanation.
With the first castle on SotN and all of Super Metroid, you can only go through certain areas after acquiring certain abilities. Symphony of the Night's true ending unlocks the inverted castle though, and imo, the inverted castle is where Symphony of the Night falters. The inverted castle seems to be thought out if you think about it, but the way it plays feels like it was just tacked on. When exploring the inverted castle, it feels like you're just filling up the map and nothing more, unlike the regular castle and Super Metroid where you're actually making progress all the way to unlocking the inverted castle. The inverted castle includes unique items, new bosses, unique items, and a harder difficulty until you unlock one of the more op weapons like Crissaegrim, but it still feels like a tacked on experience compared to the rest of the game.
If you were to compare exploring the first castle on Symphony of the Night and ending the game without unlocking the inverted castle then overall the game is a much better experience in my opinion.
So my answer is mixed. Symphony of the Night is the better game, but in terms of overall experience and progression, I'd have to say Super Metroid though.