My biggest annoyance: letting scripts control the history. I can imagine that someone thought "oh it'll be nice, you can use it for pages of an app". But the reality is that people are not nice and it gets used maliciously all the damn time. It should not be allowed.
The web should be a method of delivering documents exclusively, and be limited to the kinds of things you can do with other computerized documents (the basics, but also Audio, Video, Animations, hyperlinking, etc.)
I'd be okay with locking these heavily-abused features behind a "web app mode" that the user has to enable on a per-site basis. It should include a restriction forcing all content to come from the same origin, so that the browser in that mode won't make it easy for web apps to include third-party tracking or advertising.
I'm not against animations in UI design but these should be used purposefully to direct the user's attention on something or for minimal aesthetic effect. When everything is moving it's just like adding a ton of ketchup to everything.