I really don't know if I can fault ANYTHING in Symphony of the night, as far as I am concerned, that game is near perfect in concept and execution. I do agree that replay value, once you got to know ALL secrets is non-existent... yet getting to know ALL secrets without a good walkthrought is nigh impossible. A normal gamer will maybe get to 40-50% completion rate and will fell like he got more than his money back in playtime.
Now, as to Super Metroid, I don't feel that game offers way different replay value than Symphony of the night. Sure, you can cross some obstacles multiple ways, there is still some ability gating involved. And once you have seen all the game has to offer, few people will feel the need to go and play it again (until they dust it off decades later and play it for nostalgias sake).
I think the secret of good Metroidvania games is to give players an "open world" to walk around in, and plenty of reasons to revisit levels (which Symphony of the night does quite well thanks to the ability gating, and cleverly hidden secrets), yet also give enough narrative and story driven level progression that the whole thing does not feel like an empty sandbox.
This is where the ability gating comes in handy, because you offer the player a completly new expierience when he gets the key for a new sections, that is shown off at full swing immidiatly... while in Super Metroid, you often visit strangly empty and deserted places, only to revisit them later and find out that the enemies only have been added to the level once you trigger certain story events. Which, given later enemies would be pretty hard to beat with a less upgraded Samus, makes perfect sense.
Now, I think the solution Super Metroid has chosen for making sure you don't run into high level areas with low level gear, yet you are not 100% gated from reaching areas that are not yet important to the story, works fine for Super Metroid, BECAUSE its weird and wacky space pirate hideout which should be spoky, half abandoned, and run down. Running into empty rooms and sections which are oddly deserted only add to the expierience.
In Symphony of the night, you could probably go for something similar. Yet the game is much more going for the WOW factor. Those cool colloseum stage with the upbeat music would look EXTREMLY weird, if the skeletons and other enemies wouldn't be there to add some life to the scene. That is often not a problem in Super Metroid, most stages look deserted or rundown anyway, and the music is most of the time more muted... it fits a stage without enemies or just some small critters quite well. Actually, the big baddies are often sprung on you as some kind of suprise.
So I think both games go for a different FEEL, and besides graphics and sound they also use game design to get that FEEL.
Symphony of the night would feel weird if you could just walk into Draculas Den to find out, nope, hes not in today, gone grocery shopping. Also, one of the important aspects IMO in SotN is your character is no mere human, he is a powerful undead (half undead?) from the beginning. He is not scared of ghosts and monsters, he is one himself, and seems to not care about his own existence. So pretty much the game is about a badass characters walking into a castle of monsters, and slaying the waves of monsters that attack him.
SotN ir pretty much about finding the needed keys to make progression, and getting to new areas of the castle are the mark of that progression above everything else. In the end, most abilities are kinda useless in combat compared to a high level alucard with some of the endgear weapons and protective gear (only thing which IS kinda broken in this game.... Crissagrim Sword and 2 X the +15 defense necklaces = god mode). The only way how stuff like the bat mode add to the game is by making Alucard dependend on that to reach new areas.
Super Metroid on the other hand wants to give players that aliens feel. You are a capable soldier, but just a human being, and with the odds stacked against you. You are walking through empty corridors only to be jumped on by powerful aliens. Its a very different feel the game aims for.
gives the player plenty of things to do with those new abilities besides reaching new areas. Yet Samus cannot really level up, and you never get such game changing weapons and defensive gear like you do in SotN. So those abilities are essential in combat too, against the higher level critters. The ability to survive against those critters is the achievement here.
Personally, I like both... different games, different stories and characters, different look and feel. You cannot go wrong with either, and I don't think replay value will be increased by much by going without a lot of ability gating. If anything, it will make your job harder as you now need to make sure low level players are not insta-gibbed if they walk into the wrong direction.
If you want replay value, you need to add alternative characters (which SotN does pretty good, playing as richter its a completly different game... to bad the other alternative character didn't make it to the PS Version), add player choices having effects on the story and maybe even gameplay, maybe even go with procedural content to some degree.
Just make sure, whatever you do, story and game design reinforce each other like they do in both those games, and you are not throwing Alucard into a Super Metroid game... that would dilute the character the story is going for.