In a top to bottom typical notebook, you will have to run the notebook from the top. There is a menu item for that, of course. However, what if you also have some cells in there, which do not have to be run? They will waste time unnecessarily or even worse, will change the result. So you will need to take a look at each cell to make sure you really can run everything sequentially. Either the notebook has to be created to make sure, that running top to bottom always works and gives the same result, or you will have to look at everything. When code segments can define their dependence on other code segments, they can be designed to that it does not matter which one you run, it will always give the intended result.
As a counterexample, some things are not important but have to be mentioned. In English, these things end up in the appendix. In Pluto notebooks, these things can be moved to the bottom.
Another benefit of less strict ordering is when debugging. Sometimes cell A fails because of cell B. It can be useful for debugging to temporarily put these cells next to each other
(1) This is better to me, because it makes notebooks more consistent and easier to jump into. I read english prose sequentially, why not code?
(2) You can do this in all environments I've used with <a> tags.
(3) this would be nice, but I'm not sure it's worth the tradeoff because the editing environment wouldn't correspond as well to the exported document.
(4) true, but I have a vim plugin that make it better
(5) also true, but this is a good thing for simplicity. I don't want to have to keep track of the lexical scope of multiple language environments
(6) There are tools for this, but yeah it's not great. The main issue is saving outputs
It sounds like the goals of notebooks vs org mode are slightly different, at least the way I use notebooks.
For me, notebooks are a tool for sacrificing control and programming flexibility in exchange for easier collaboration and visualization. It's harder to write structured code, but it's much easier to share with a large number of semi-technical people.