Ubuntu – Partially hidden workspace indicator in Ubuntu 17.10

You rely on a couple of flawed assumptions. First; it is not obvious that Mark Shuttleworth makes all these decisions. I hardly believe Ubuntu would've become such a success if he was a one-man show. It is a collective effort. Also, you assume that "this really handy function" has been thrown away. It hasn't.

Ok, now let's look at your question. It seems to be about how to launch a new instance of Firefox when there's already one running. Easy; middle-click it. Or if you use keyboard shortcuts, append Shift. For instance, if Firefox is number two on your launcher, press Super+Shift+2 to launch a new instance. You can then use Super+BAT (button above tab) to switch between Firefox instances, and you'll be moved to the correct desktop if they're on different ones. It will remember the window order, so you will also be able to use Alt+Tab to switch between the most recently used instances per application.

The cube and other Compiz effects are still available. Unity itself is a Compiz plugin, so none of those options have been removed.

To an extent, you have to adapt to the working environment you choose to work with.

1) a grid of workspaces (3 columns, 2 rows to be precise); You already found the Workspace Grid shell extension

2) the application windows remaining in the workspace I move them to; Using Gnome Tweaks, which is not installed by default in Ubuntu, you can set workspaces to "Static". With dynamic workspaces, workspaces automatically are removed when they are empty, so indeed an application you placed on workspace 3 may end up on workspace 2 or 1 later in the session.

3)miniatures of the workspaces content in the switch modal; Gnome-shell provides miniatures of the workspaces in the overview when you press Super. By default, however, you have to hover the right side in the overview to make the miniatures visible. You can make sure the workspaces are always expanded with the extension "Always zoom workspaces"

4) workspace switcher showing the overview of all workspaces. I do not follow here: in the overview, all workspaces are shown. You may also install a "Workspace switcher" extension that provides a clickable icon on the panel that allows you to switch workspaces from a pull down menu.