I feel a little silly for suggesting improvements, since they're probably on your to do list already and it is probably a funding issue, but here's what i suggest just in case it's helpful since i love the idea of this game;
1) more big, flashy graphics (i.e., showing a meter filling up and deflating
2) actual animated bad guys that creep onto your screen when you aren't expecting them and try to get you to do bad things
3) more ease of use, but I've no idea how to accomplish this. It just feels like if you have allies and you're also doing your own thing, there are a myriad of button/links to click to remember to do different things. maybe the science lab and other things could be brightly colored potion type bottles that titter as if about to fall when they aren't clicked on in a while. also, perhaps you could have info for the different quests show in a hover bubble instead of having to click on each one to remember what it was.
4) the power-ups and bad guys don't really feel like they're connected to the quests. somehow it needs to visually show us how its helping or hurting.

Lastly, just thanks for putting so much effort into developing the game thus far. I'm really excited about it and about what it could become and about all the other potential applications for gaming.