The biggest problem with Aquaria is it simply never got a lot of publicity. I have shown it to so many people that ended up loving it, they just honestly never knew it existed.
The thing is, Aquaria could still succeed and make them a ton of money - they just have to reach out and let people know the game exists! Because the problem, even today, years after it came out, isn't that people have heard of it and don't like it - people simply haven't heard of it.
I pretty strongly believe that even now, if Alec or Derek actually reached out to one of the loud voices in the gaming community, and got them to back Aquaria and spread the word that "hey this game exists and you should play it" it would still take off and be a massive success. They could do this, too - think about it, if one of them reached out to Penny Arcade and got them to talk about it.
Minecraft existed for years, and then PA had one set of comics about it and some newsposts, and *then* it took off and became popular. Aquaria is in a similar position of that very few people that actually know about Aquaria, dislike it. There's no reason to think this wouldn't continue if more people knew about it.
And it's aged amazingly well - a lot of people I've shown the game too, are absolutely stunned when they find out how old it really is - it's the type of game that is so good, and so high quality, it could've came out this year and people would believe it.
In short - a kickstarter for Aquaria 2 would fail just as Aquaria has, because most people simply literally do not know Aquaria exists, to support a kickstarter. Before anyone tries to get support for Aquaria 2, they need to look at getting people to even know that Aquaria 1 exists and spread the word about that.
Honestly, so much could be done for the game if PA, or Yahtzee, or someone with a large viewerbase, were to talk about the game.