Though neither mode is perfect in all situations, on balance I prefer focus-follows-mouse.
I do NOT care for copy-on-select, I like copy to be an explicit action. That way I can select, copy, select, paste to replace. With copy-on-select, you have to select, paste, select, delete which is less natural for me.
copy-on-select is great as long as the other clipboard still exists too (this is typically the case in linux). What is the downside, if you can still ctrl-c/ctrl-v to a separate clipboard?