I want to preface this post with my thanks for all the constructive feedback. Although I may take issue with certain aesthetic stances expressed in this thread, I appreciate that all of you have taken time out of your busy days to try to help me out. Having said that....
If she is supposed to be whimsical and cutesy then you have a problem but if she is a little more brash then its not so much of an issue.
I would not say that cutesy and whimsical are necessarily in the same basket, but I think you hit the nail on the head that in graphical adventures we (rightly or wrongly) judge character based on appearance. So my agent has to be tough, and she has to be proud, so she's going to carry her head high, whereas the more demure feminine ideal is to kind of look downward.
Maybe my former paint-over was a bit too realistic or something, so I made this very quick and rough sketch to illustrate the typical exaggerated "cute" ratio used in cartoons:
This one isn't anatomically correct - it's basically a big ball with eyes on - but it conveys positive things like friendliness and a childlike cuteness, often found in pixies, I'd guess.
OK, so she's got cutesy proportions. But she looks kind of shy and sullen to be breaking up intermagestical espionage rings. As Cailin said, she's got to look the part.
There's been some question (and confusion) about combining proper anatomy with a pleasing visual aesthetic so I made a little tutorial to help you and others out. I'll go through and explain each of the steps in detail and you're encouraged to follow along. The idea is that, while anatomy is important, you can and sometimes must take liberties at times when dealing with very small images to get a visually pleasing result.
OK, I get this. And theoretically it is a very well proportioned face, although somewhat old and masculine looking for my purposes. Love what the shading does to bring out the features, btw, but I can't be spending that kind of time on individual frames if I'm going to finish this project in my lifetime. So stylistically I'm sticking to the line art (it works well with vectors anyway).
The only reason the signals are mixed is because the head is so anatomically deviant it's hard to name the parts properly. When it comes to crux of the matter - that your pixie looks neanderthalish - I think the signals are pretty clear.
So... I'm really having a hard time with the "anatomically deviant" label, especially given that this sketch was offered as an improvement.
Why must the attractive female have a bulbous forehead and ridiculously oversized eyes? Why must their infantile faces be squished into the bottom-most quadrant of their heads? Why must they look downward, or at least tilt their heads down demurely? And why the small mouth, no-jaw aesthetic? These features may be considered to be beautiful by some, but the characteristics they evoke are insecurity, vulnerability and weakness. Some men may find this attractive in women, but this character needs to be stronger than that.
Sorry, but she does look sort of deformed. When you look at the average head in profile, the foremost point of the forehead is roughly vertically aligned with the chin.
But what if she is holding her head up proudly, like a soldier. Here is a simplified version of my process with some random feminine profiles procured from the internet for the purposes of demonstration. Models were selected on the basis of a) having a full-profile picture and b) holding their heads up proudly. It so happens that I think all three are reasonably attractive human females, but we are all entitled to our opinions.

What I have done is trace my model's face and main features in a simplistic fashion: eyes are just circles with a brow line and a white dash highlight. The ear must be oversized to make it obvious that she is a pixie, and the eyes need to expanded or they will only read as dots at my game's resolution. Expanding the eyes downward makes the nose appear to be too high and making the characters look dumb, so my only option is upwards. This is a 200% zoom.

I must then play with the features a bit, due to the way that vectors are compressed. An eye can easily bleed into a forehead, etc. so features must be separated sufficiently so as not to look awkward at 100%. Here is the result:

In conclusion, I don't think the "anatomically deviant" label can really stand up to evidence. This is in fact how human females do look, admittedly with crazy hairstyles and certain feature accentuations required by my game characterizations and resolution. I think this style suits the "feel" of my game, and makes my characters appear both human enough to be beautiful but also exotic enough to be believable as a magical species. I think comments like Daniel Thomas's are fair and constructive, as such feedback can improve the art without compromising the style. But I take issue with the relentless assault on my drawing style and aesthetic beauty of my pixie. I challenge anyone who thinks I'm that far off the mark to make their own pixie-game. With blackjack. And hookers. On second thought, forget about the blackjack....