You used to have to login separately every single time

Are you sure that wasn't a problem with your browser? Either way, you can still watch the vast majority of videos without signing in. If you want annoying logging-in experiences, try looking at NSFW videos at...Daily Motion, I believe. Drives me up the fucking wall.

taken down for a violation of the terms of service

So? That's a good thing.

or copyright (or not available in certain countries).

To comply with law...

And I don't think these take downs have decreased significantly either.

The in-video ads and the ads on the page were just horrible

These make the site actually financially stable.

Half the videos were taken from somewhere and some asshole added a 10 second "intro" with their bullshit logo, then they played "Let the Bodies Hit the Floor" over the entire thing

This isn't a user-experience thing. This is kinda like not using imgur because people upload a lot of rage comics to it.

They have the little popups throughout the video (which you can disable but who can be fucking bothered).

This is actually somewhat annoying. But yeah, I haven't bothered to disable them either.

There's really only a few things I'd change about youtube if I controlled it. I'm not going to delete those annoying "Let the bodies hit the floor" videos, because that's just pointless censorship. I would delete pornographic videos so people would advertise on my site. I would have ads because hosting all those millions of videos results in a LOT of bandwidth usedup. I'd comply with the law.

If you go on other sites, they're much more annoying. The layouts are worse, ads are much more numerous, they automatically redirect you to another advertising video when your video is finished, the actual video controls are less intuitive, the video loads at the highest rate by default which sucks if you have a shitty connection, the slider is extremely imprecise, the recommended videos are rarely relevant and usually just ads, etc. With Vimeo you can't even skip past the buffer.

I just consider youtube a breath of fresh air, honestly. One major criticism I have, however, is the difficulty of browsing a specific user's page, and there are bugs when it comes to the comments (which usually aren't worth reading anyway).