How about change the main behavior of the "dock" on Shell?
When the favorites bar is full, the icons turn to a very small size, which is hard to manage. I think this could work in a better way, just like a regular dock, with zoom when the mouse cover the icons or make this bar higher, like Ubuntu does nowadays, but even in this case (Ubuntu), the problem remains, it just let a longer time to show up. In some cases, the icons who indicates the app in execution can be almost the same size of the icon itself.
Another possibility is to change the "frequently used" page on the dash to a "favorite apps" page, then, the favorited software will appear in this region and the bar only handle opened apps.
Edited by Ghost User