The core reason for me will pretty much always be just how immersive the game was, and this was due to the incredible soundtrack that managed to be all of chill, upbeat, and even somber at times. Totally helped give the game a sense of awe, at the right times, too. The atmosphere and environments were also incredibly well done - everything just really helped give the game life. The ocean actually felt alive, and I came to actually care about Naija, as opposed to castlevania where the castle just feels like an inorganic place to fight, and I never cared about the avatar beyond gameplay terms, there was so much more here.
On that topic, Naija is surprisingly an incredibly strong character, and more than that she's got to be one of the strongest female characters I've seen in a game, and that's impressive. She manages to fulfill almost none of the stereotypical cliche female lead roles - she's strong without being a femme fatale or something overdone like that, but also doesn't fall into the trap of being TOO weakly feminine as happened to Samus in Metroid Other M. It's quite the feat, what was done for a character I was originally expecting to be little more than a shallow avatar for the gameplay, like in most metroidvanias where the gameplay is the main focus.
This sounds like I'm not picking a core reason I liked Aquaria, but I really am - all of that ties strongly into making the game incredibly immersive and just real, and so it all needs to be mentioned. It was the immersion that was the core reason, not solely the soundtrack, or the writing, or the atmosphere, so I can't name just one of those.