Alt+Tab on Fluxbox

For some apps (e.g. file-roller) this can be fixed by changing the StartupNotify key value from true to false in their respective .desktop files (e.g. /usr/share/applications/file-roller.desktop).

The above doesn't work for all apps (e.g. nautilus) so another way to fix the problem would be a custom shell extension; just to give you an idea, you could easily fix nautilus behavior like this: edit /usr/share/gnome-shell/js/ui/windowAttentionHandler.js and add these three lines of code:

    if (app.get_id() == "nautilus.desktop")
        Main.activateWindow(window);
        return;

after the following line:

    let app = this._tracker.get_window_app(window);

so you end up with something like this:

    let app = this._tracker.get_window_app(window);
    if (app.get_id() == "nautilus.desktop")
        Main.activateWindow(window);
        return;
    let source = new Source(app, window);
    Main.messageTray.add(source);

However, it's not worth writing your own extension unless you want to target only some specific applications. For a global change it looks like there is an extension:

just show the window

that overrides the "notification system" (it works fine here on gnome 3.8).
Keep in mind the two files (extension.js and metadata.json) have to be placed in:
~/.local/share/gnome-shell/extensions/justshowthewindow@ryanlerch.org
Activate the extension via tweak-tool and restart the shell (Alt+F2 then r then Enter).

I also struggle with knowing which window has focus (irrespective of how it got i).

I have switched on the glow feature of oxygen theme in KDE's plasma. I now have a different glow around active and inactive windows. I also set a matching title bar colour. Green for active, and red glow / gray title bar and border for inactive (but the borders are very thin).

It has made a big difference.

I also set meta+tab to lower window (and move focus to new top window). No animation, just simply the glow moves.

I then added an effect to move slide back windows: window move (temporarily out of the way) to let the other pass. This helps me keep track of where things have gone (a sub-conscious hint, linked to real world physics).

I chose KDE plasma for these features. (You can install it and probably start it (replacing cinnamon) without even logging out.)