I know this comes a bit late into the topic, but I just wanted to share my thoughts to Alec about people's complaints about the game.
1. "I hate Li"
The problem with Li is that we never really learn about this character. The game is really suppose to be about Naija, and the storytelling is centered around Naija, and we play fully as Naija most of the time. Li feels a bit like having an extra tentacle sticking out of your back. Sure, it can be helpful sometimes, but it still feels a bit unnatural. He's not developed enough to be a major part of the story and his help is minor at best. Developing him more would have fixed the problem, but at this point it'd be difficult to change him. He's something that you need to learn from when making future games. Don't feel like you have to fix him now. Aquaria may mean a lot to you, but unless you feel like Aquaria is going to be your only major project, you need to let it go. Any changes you make to him at this point could make the game worse. In other words, just let it go.
2. "Menu screens suck"
Some people will complain about anything. Don't worry about it. These people are stupid.
3. "I hate dragging things"
Auto-cooking stuff is stupid. Part of the appeal in the cooking system is it's flexibility and options. If they don't like the system, that's their problem. However, some interface enhancements are always helpful, like letting people double-click items to move them to the cooking area rather than making them drag everything.
4. "Map System sucks"
The only problem I had with the map system is that you had to move to other areas to see what you had and hadn't explored. Being able to see all explored areas of the map at once is helpful. Think about how the Metroid/Castlevania games did their map systems.
5. "The story is too obvious!"
6. "The story is too vague!"
7. "Mia plotline is stupid"
You can't please everyone. Don't feel like you have to.
8. "I'm lost, I don't know where to go"
This must be the first time they've played an exploration-adveture game (aka a Metroidvania game). They need to grow and pair and deal with it. Or not play games of this genre. I don't play turn-based RPG's and then complain to the developers that I have to deal with that battle system. It's a personal preference. If you try to address this, you will break the game. Now, common stumbling blocks can always be subtlely improved (like the throne room puzzle, or that song puzzle in the sunken city) but addressing this problem in a global sense is impossible.
9. "I'm not going to buy the game unless it has widescreen support"
Good lord I hate people like that. At least this is the kind of change you can make without any blowback. Pretty sure there aren't any people that wouldn't buy the game if it had widescreen support.
10. "I'm not going to buy this game unless its for the Mac"
I've got a friend in this situation. She has a Mac laptop that she uses. She is in this position. She really wants to play it. She doesn't have a choice in the matter unless a Mac version is available. I'm glad you're doing this.
11. "I'm not going to buy this game unless its for Linux"
Now this one is a bit harder to justify. From my experience, most people that use Linux have a separate Windows partition anyway to deal with compatibility problems. I know my brother is like this at least. Don't feel like you have to have a Linux client because you'd be catering to a very small audience. To be perfectly honest, your effort would probably be better spent trying to get the game on PSN/XBLA/WiiWare.
Alec, you need to realize that you've still created one of the best indie games ever made, and in my opinion, the best indie game ever made. That is a tremendous accomplish.
However, you also need to realize that almost no game is perfect.
You can't satisfy everybody. You can't please everybody.
But you can certainly satisfy and please a hell of a lot of people.
Don't take individual criticisms seriously. Now, if tons of people are criticizing a certain element, than it certain merits a second look. But just people one or two people on the boards complain about something doesn't mean you have to change it.
Don't take this stuff personally.