Despite any criticism I might have, I'd still like a sequel even if it was done the same as Aquaria in almost every way. (although a new gameplay style would be nice)
I'm sorry that Aquaria has been too difficult to repeat the process, but aren't you going to get that with ANY game you make?? How is the current game you're working on going to be spared from criticism? Is it because it doesn't have a forum? You could just close the forum.
I don't want to say the issue is irrelevant, just that it's not irreconcilable, and that I think you'll still have to deal with the issue if you keep on the profession of game-making. (I don't know if you have other jobs, like music composition or music playing; and whether they're free from criticism or just of significantly less criticism...)
IMO, Xenogears had a pretty terrible story, and the storytelling was even worse. It even degraded into a novel at the end. (I'm guessing they ran out of time to finish the game properly? They just ended up having large periods of text followed by a single boss or single dungeon)
I enjoyed playing through Xenogears, but I can't for the life of me remember anything about the plot, because it was so convoluted.
I think Aquaria relies a lot on the player's imagination to fill in the gaps. Its a more subtle/light way of telling a story. I guess the downside of that is that some people fill in the gaps with "OMG IT WOULD HAVE TO BE THIS STUPID THING THAT I HATE LOL".
Oh well, you win some, you lose some. You can't make people who are determined to hate something like it. 
And that's one of the main reasons why I don't ever want to have to make a sequel. 
I haven't played Aquaria recently to re-evaluate how your story-telling relates to any of these issues.
On a similar note about leaving things up to the audience to imagine, I get pretty sick and tired of the TV show Lost doing that, but they give no hints at all.
I do think there was some cheesiness in the voice acting. Over-dramatic in places.
I think voices in games are a lot more demanding than text. With text you can imagine the voice in your head however you think it would be most appropriate. When you hear a voice, it's no longer tailored to you. It's just more difficult to get voices right than text, I think. There's just a lot more variation.
Aquaria is a unique story in the way that it's told, and this all relies on the player. There are some people out there who are too dense to look beyond what is presented to them to what it truly means. To fully get the meaning of some events, you have to look deeper. (ie: Naija finding Li symbolizes an end to Naija's constant loneliness, but some people would only see this as "oh wow she found a boyfrnd")
No, I think the end of loneliness was literally in the dialog. No reading between the lines required there.
Also, while we don't get any build-up to the romance, we do get a flashback that they've met at least briefly before.
If it hadn't been for Li running away when they "first" met suggesting otherwise, there might have been the possibility that they had spent time together.
I wonder if Li meeting her as a little girl while he was in a boat is the reason for him remaining there and diving. (unless he was just stuck there with no alternative. :> )