I always find that I agree and disagree with these kinds of comments. From an accessibility and standards point of view, I absolutely agree – don't fuck with what people understand. From a progressive, artistic point of view I think these kinds of implementations allow for some creative expression. In the end, all industries have the artsy take on what is possible, but not necessarily ideal.
As with most things, it's all about balance. Is the atmosphere of your web form worth losing 10% of its conversions?
If you're designing MYST for the web browser; probably. If some small percentage of luddites can't get past your fancy character creation screen, then the game is (likely) not for them. Their frustration is worth it for the total immersion for the ones that can. There are a number of environments in which a cohesive experience trumps the drawbacks of a fiddly interface. But if someone is wanting to convert sales of a B2B accounting application, or needs to create batch data entry forms for said application, then things need to be weighed differently.
Being a good designer isn't about knowing how to recreate [software from the 90s] in Javascript or CSS3. It's about making lots of little decisions like this all the time.