These are UI complaints that can be addressed with a bit of investment and thought, but it's unfashionable work - Mozilla even tried to outsource it to Pocket, sorta...
> Bookmarks are subject to link rot
That can be fixed pretty easily: when the user bookmarks, submit a job to the Internet Archive, then use it whenever you get an error page from that link. FF already does half of it with the experimental no-404 extension. Alternatively, you can have your own InternetArchive-like service to do that, which is basically what services like Pocket and Pinboard do.
> having more than a hundred of them is a timesink nightmare to manage
You don't really have to manage them - these days they show up as soon as you type in the address bar. Ideally you'd have some sort of AI-powered categorisation system auto-filing them in dedicated folders, which could probably work with a bit of specialized meta tags. It's basically the age-old problem with filing documents of any type.
> bookmarks are useless when you are offline
Yeah well, a browser is also kinda useless when offline...