HTML, CSS, and Javascript are 3 completely different technologies (or whatever you want to call them). You don't need to use CSS. You don't need to use Javascript. But they help, a lot.
Bootstrap or Foundation are options; they're not requirements. React or AJS or Vue are options; they're not requirements.
You can build a perfectly good website with inline styles and native JS. You don't need to transpile typescript to JS. You can write, native JS all day to your hearts content.
We can look at almost any other programming language and say the same things. If Swift is JS and Interface Builder is HTML in iOS - you don't need to use Interface Builder. You can build your entire interface with Swift in code. Is it a good idea to do so? Maybe, maybe not. Sometimes, interfaces can only be built via code due to their complexity, but it is an option. The same way sometimes you need to have JS output HTML because HTML by itself won't cut it.
tl;dr - no, I don't think HTML / CSS / JS are broken. Their the foundations of web development. I do think frameworks and everything that goes with them are broken to a certain point but that's a whole other conversation.