Okay, even though this explains some, it also doesn't, it's not answer to if Creator made it or if the city crashed. Yes, I already knew Aquaria is a bit 3d, multiple layered, seeing you have open waters and caves, which reminds me a bit of Metroid again, but I just think of Metroid too much.
And about the door. It still opens. I mean, what door still opens after crashing hard? And IceD like you said: "Everything we create, no matter how huge it would become, won't stand the test of time and will finally turn into dust an rubble.", so did the ruins from the city. At the beginning he wanted to recreate everything, but after long times he saw that everything slowly became corrupted and stuff, well, so did the city.
I still hard believe that the creator recreated the city, just because of the reason that it is almost impossible that it's very deep in the ocean, even under the most things.
And well, earthquakes exist, but that would make the ruined city even more rubbled.
And about the door, he just wanted Li with you to annihilate him, right?