I used to be a Flash developer, now a Javascript developer. Everything that was raised as an issue with flash (except web's open nature) is now an issue with Javascript development today. Preloaders, skip intros, single page apps, browser back button issues, SEO incompatibility. all of it. loving this.
The point is not (merely) the technology behind it, it's the agencies' model of selling the customers "rich internet sites" whose main point is to show off to other people that you have pockets full of money.
A good intro can help to sell your site project to a customer (and help them selling it to their superiors), but no longtime user would protest if you took it away.
Single page apps are a way to fit in an interaction model that doesn't fit the idea of "one address, one page, one text" that was the idea behind the Web in the first place. So, yes, you give up some of the benefits of the Web (navigation with bookmarks, back button) or have to fight hard to get them back, while keeping others (mostly, platform independence and a built-in client-server architecture)
