A pen is a pen no matter what brand it is and it is a universal tool that
anyone can use. With Adobe Flash being used with his school, I am guessing
they contracted a 3rd party company to assist with the schoolwork and that
company sold the idea that their solution is the best.
The 3rd party company probably chose Flash for the universal exposure meaning
it can be ran on any browser and operating system. It is used more than Java
and can even be run on the archaic Internet Explorer 6. If they were to offer
a more native version that used SVG, Canvas, and CSS3 animations, they run
the risk of it not being able to run on older versions of IE.
If it were me, I would probably go for the standards route and use Modernizr
to detect features and polyfill where needed. Of course using a JS library
like jQuery is helpful too as they aim for compatibility with multiple
browsers by using workarounds for each one.
Either way, the original poster may be screwed as the school may have a
contract with this 3rd party and he may be the vocal minority speaking out
against this. In other words, you may just have to deal with it or not do
your homework and fail the class.