The limitations with the tower defense game are the result of programmer laziness rather than some limitation with JavaScript itself. If the game was reworked to use sprites instead of drawing using basic geometric shapes, it would appear much more polished. The major limitations with JavaScript versus Flash revolve around dealing with media (we had to use a Flash tool to implement conceptual sound support for PTD, http://github.com/rictic/processing-tower-defense/tree/maste...), but I think these are generally being resolved with HTML 5.

To respond to your questions:

1. With some minor effort we were able to get PTD running on Firefox, Safari and IE. (Chrome didn't exist at that point.) The performance on IE 6 and (I think) 7 were prohibitively bad though, so it wasn't actually playable. Thanks to projects like excanvas, even browsers without native canvas support don't pose a big problem.

2. I don't have Flash experience, but PTD is just a collection of static files. I never felt deployment was a problem.