First of all thank you for involving everyone in the design process.
Regarding the app menu in the top bar - this change is unnoticed by me. Since I do not know any application that puts something useful in that menu, since the early GNOME shell era. As about focus - I remember when in the first version top bar menu has big color icon in that case it helps notice active window. As for now - I do not watch on it at all. But i believe am from category of advanced users and this menu marks app name + some apps still have useful items in this menu (maybe some one use it).
As for animation effect. Tested animation effect feels like satle, but after several days of testing it becomes very annoying!
+ it blurs window (I believe it could not be solved in any case).
+ it not play well with a11y requirements if user prefer reduce motion
As a solution - just a simple border around the window could be drawn for about 2 sec. It would be consistent with buttons focus effect. If need more prominent effect this border could be scaled for a moment.
p.s. window focus effect super helpful when switch workspaces
p.p.s. this effect does not help in tiling setup
Hope this helps.