Well, there is one thing I found a bit lacking in Aquaria: the lack of dynamics between Najia and Li. They are a couple after all, and I think there is a very romantic basis for the relationship of the two.
I'm mostly thinking animations, like dialogues or games between the two.
Games I think of something fun and simple. I don't know suddenly, but tag or perhaps some sort of ball game? There might be or might not be a reward, but the games have to be fun to play and simple. Don't think of any arcade-stlye games with big-letter scores and proper fields or something like that.
Just at one moment Li might pick of a peice of dead sponge or something and starts throwing it back. You pick it up (by hand, not with the blind spell) and throw it back. He catches it, and tada: instant tennis. Well, as successful as underwater tennis can be. Perhaps with a creature instead or something?
Perhaps some stuff that is typical in a relationship, like making a fuss, misunderstandings (there should be a few, people in practically identical culture have misunderstandings, two people a world apart should have plenty) someone having anxieties and yes, the big three letter act called "sex" (nothing explicit of course, hell, if I knew how, I could make a very suggestive scene with all the things that game already has).
What would be the point? Not much, just to make it look nice. Or maybe not?
On the other hand, handling the relationship can have effects on both Naija or Li, or perhaps just Li as we control Naija.
What I had in mind, is that for example, Li would be influenced on what Naija wears. If she wears something cute or lovely, Li might want to hug or kiss Naija more. If she wears something fear-inspiring like armor, he would be more braver (shoot more or make his shoots more powerful, etc). Perhaps he could also react to the different forms of Naija, I'm pretty sure I would be at least a little freaked when my girlfriend turns into a fish.
Kissing might increase Naija's health by a very little?
What I would want to see is more small animations. Like when Naija takes a nap and Li joins, Li embraces Naija or vice-versa.