Many files - good. It is easier to update the game.
3D - still show themselves in the future.
Stealing code - store information in a database.
(code in Flash is not a secret)
The introduction of malicious code - in Flash it was much earlier and continues to this day.
The absence of massive support for HTML5 - a struggle with publishers and sponsors who want to earn money on the already tested systems. Flash has brought billions of money income, and HTML5 yet. Why be afraid of the creators of games? The game is done - the game is sold. Afraid of the publisher.