I killed an hour or so familiarizing myself with how the FOW and Light and Vision functions interact, and I have to say that, despite some fantastically robust functionality (light source definitions, among many others), I have two suggestions:
(1) In the next major revision of MapTool,
centralize control of FOW, Light, and Vision on the GUI as much as possible. If possible: one spot for defaults on all three, another for active changes to all three. Consider offering "master" options that represent how these three interact: just seeing something on the menu that says something like "Light overrides FOW" or "FOW overrides Light" makes it much easier for newbies to ramp up the learning curve.
(2) Non-D&D light paradigms. It is great that you can create concentric circles of light zones, as per D&D style vision rules, but MapTool really is a paradigm shift in playing. I understand, from a game-mechanics point-of-view, why light intensity edges are hard edges, but I'd like to see radial gradient (color gradient and opacity gradient) -- so that zones can have fuzzy/fading edges. As an added bonus, showing tokens in "dim" light zones merely as black silhouettes seems very useful, too. You can do that now with some manual legerdemain, but it could be an automated feature/option.
Anyway, still an outstanding set of tools. You've been able to give more gametable functionality to our hobby than WoTC with all its $$$ and (for a while) intense corporate pressure to crank out a gametable ap. They promised the moon and delivered nothing. You promised nothing and delivered a great product. Rock on! 