As far as ideas for a sequel go, I have thought of a couple ideas (like everyone else I'm sure).
I imagine it would be primarily Lucien's quest to locate his mother. Li would show up too, possibly as a gadgeteer/advisor who gives you important information about the world, along with mechanical gadgets to help you along. You'd have to include a major female character too, of course, since one of the biggest strengths of Aquaria is its female hero. I'd suggest Lucien's girlfriend (let's call her-- I don't know-- Nani, for now). I't'd be kind of neat to make her the bruiser of the game while Lucien is the more cerebral, gadget-using part of the team.
Mainly though, I like to think about what kind of levels you could put in a new game. The underwater world was the biggest draw for me-- particularly the Kelp Forest and the Abyss. But there's many, many more places a new game could go, such as:
MANGROVE FOREST: Complete with big, arcing aerial roots to climb on. Creatures would include: Mimic octopi (that could change into facsimiles of other creatures), Manatees, Puffer fish, Sawfish, Crocodiles and Cownose Rays. It would have a tide effect that would cause the water level to rise and fall like the pathway to the Sun Temple boss.
TEMPERATE TIDAL SHORE: Lots of little pools along a rocky coast. Hazards would include slippery wrackweed, sharp barnacles and dive-bombing seagulls.
HYDROTHERMAL VENTS: Although Aquaria already has an Abyss level, a sequel could have more specialized deep-ocean settings. Would feature Yeti Crabs, Tube Worms, Eelpouts and giant, sulfur-belching Mussels
RELIC SEA: An isolated sea filled with prehistoric (Cambrian-age) animals like Anomalocaris, Opabinia, Wiwaxia, Hurdia Victoria, Bannfia, Odontogriphus, Eldonia, etc.
