IMO, if they want to make a "Symphony of the 2.0", they just need to capture the atmosphere of the castle again. The problem is that atmosphere can be one of the most transient things in game design.
I didn't play Symphony of the Night when it first came out. I always had Nintendo consoles, so I got to AoS, DoS, and PoR before I ever had a chance to play Symphony of the Night on my PSP. I'm just going out of my way to say this because sometimes "atmosphere" is just another word for nostalgia, but Symphony of the Night really did have it in spades were its successors didn't.
A big part of it is the castle design. Aside from the lack of reused enemy sprites that the later games became notorious for, the castle itself is very unique from location to location. Very few rooms are copies of other rooms, or even similar to them, both layout-wise and art-wise. Backgrounds are very identifiable and most rooms have design elements or set pieces that make you say "Oh, I'm in THIS room". And with all the little details added in addition, it makes the castle seem very real, like you're actually exploring a building something built that creatures are living in and not a series of rooms divided up into sections (see "levels"). There were even whole sections you could miss and not even realize it. Now, obviously the other Metroidvania's weren't entirely copy paste, but their castle's weren't nearly as well thought out as Symphony's.
Adding onto that, the music drives the atmosphere way more than the other games. It is grandiose and dramatic at times, hopping and jazzy at others, and even soft and sad as well, but never really delves into the gameyness that the other Metroidvania's could. I think AoS might have been able to replicate this if it had better hardware, but the GBA just can't output that kind of sound. You can hear the compositional shortcuts Yamane had to take, and I don't know whether it was the hardware or just the influence of working on the GBA, but her compositional style totally changed from Symphony of the Night to Order of Ecclesia. IMO, the music became less atmospheric and more focused on itself. A Metroidvania that had a soundtrack like Lament of Innocence's would knock it out of the park.
Because really, mechanically, Symphony of the Night probably has been surpassed. The Soul System trimmed the fat from all of Alucard's numerous, numerous, and sometimes pointless options. Spells, familiars, relics, sub-weapons, weapon abilities, and what have you all became different souls to collect, instead of filling up vast, various menus of different abilities and items where half would probably only be touched a once or twice. Sure, there were great items like the shield rod, the spike armor, the capes, the muramasa, and others that had some real personality to them, but there was also a lot of clutter. Not to say future Metroidvania's didn't have their crap skills/items, but you could tell the thought process behind a lot of them was "Well, it has to have a soul. It can, uh, fire, er, another projectile?" Symphony of the Night sometimes just had item clutter. If anything Order of Ecclesia did a very good job of only giving you abilities that had a purpose, now we just need a game that brings the character that Symphony of the Night had back to the weapon and combat systems.