SoTN is a fantastic game, and it did a great job adapting the Metroid style to the CV formula. The only problem I would say, is that Konami STUCK with that style almost exclusively for their 2D CV games from then on.
It's hard to say, SotN is one of the best games ever made in my opinion. Not THE best CV, to me that's Super CV 4, hands down. Amazing game, top to bottom. But SotN is up there.
But as for best "Metroid-vania style game ever"? Sorry, but that has to go to Super Metroid. Not only did it pave the way (after Metroid 1 and 2 set a VERY good prototype standard), but as a game it is basically flawless, outside of a "takes some getting used to" wall jump mechanic. It's fun to explore, the world is compelling, the atmosphere, the graphics, the ambient soundtrack, the boss fights, everything about that game was nearly flawless, and incredibly memorable. It wins, just by virtue of being so goddamn good.