"Over the years, I've done a lot of work with games and simulations for training."
OK. That really doesnt have anything to do with the web, however. Sure, the web can be used to deliver the project - that doesnt mean it has to actually run inside the browser. There is a HUGE difference.
"We could not have produced this educational game with just HTML."
I get where you are coming from but I still think it's far off the mark. The web is not a game platform, that is not it's purpose, so 'we could not do games this way' is not a very telling criticism.
You can use better tools to make the games, and use the web merely to deliver the game. Where is the problem with that?
It would NOT be slower, clunkier, or more prone to error. It could be done using exactly the same technologies in virtually exactly the same way - the only difference would be very slightly less easy to get it started, and in return for that, your browser is no longer a malware vector.
Or, it could be done using technologies better suited for the purpose, in which case I would expect the results to be less clunky, faster, and more stable - but the development process would be more expensive as well.
I get why you would want to use RAD to lower costs, just not why you see the tiny convenience of running in the browser automatically as worth the cost of turning the web into a malware distribution network.