For the kind of specifications you're describing here, I'd recommend Flash as the best way to go. As you mat have already discovered, irregular and complicated shapes and conditions are pretty time-consuming to handle in Javascript. Okay, as a Flash developer, I'm biased, but I genuinely believe this to be the case:
* In a Flash IDE you can draw/trace/convert to vectors any shape you like, e.g. map, photo or drawing, and attach an event listener to it.
* You can listen for mouse click, double-click, down, up, over, out and x-y positions.
* With Flash Player 10 you can also listen for touch-screen events.
* The Flash Professional IDE is used by designers and animators to create highly complex, layers, object oriented graphics so it goes without saying that it's easy to use and more than capable of producing what you need.
* If you're an Actionscript developer, you can also manage loaded image data at a Bitmap level and you have complete control over it, making it possible to automate certain activities and features very easily.
* You can separate the application from the media and have Flash "templates" that, via XML, load images and lesson data to automatically generate learning interactions.
* Flash is a compiled language and so runs much faster than Javascript, enabling Flash applications to do much more complex calculations.
* There are lots of 3rd party web services, e.g. Google and Yahoo!, available for Flash apps. to consume. Loading maps and the full range of map data would be no problem at all.
* And lots more...
Some of the best things that Flash can do are not strictly SCORM compliant. You can use SCORM to deploy Flash which is useful if you want particularly detailed activity and grade reporting, although AFAIK, Moodle doesn't support all of it, and there's also the option of using the SWF Activity Module: http://code.google.com/p/swf-activity-module/ which provides Flash applications with most of what they need to integrate with Moodle and web services automatically.
Just my €0.02!