Yes, the favorites.ini file was, in the past, a place where you could specify the engines you use most frequently, by copying some entries from the engines.ini or retro.ini files in order to have a shorter list. This was changed in v3 when we started incorporating other engine architectures such as Linux and Windows x86, Python script, historical, etc. which were placed in the favorites.ini file and the name of the menu entry was changed from Favorites to Special & Historical.
I don't think it would be difficult to re-introduce the old behavior. You could do it by moving all the current favorites.ini engines into the engines.ini file and revert the menu entries back to Favorites from Special & Historical. Then copy your favorite engines entries into favorites.ini.
But I think a better solution is to leave the current structure and add a way of designating specific engines as favorites and reintroduce a favorites menu entry which can read and list them.
Of course, whatever the community decides is fine with me.
Randy