Since going forward all themes in the theme repository will have to use the customizer for everything https://make.wordpress.org/themes/2015/04/21/this-weeks-meeting-important-information-regarding-theme-options/, I would expect any other functionality that have done similar things to be deprecated from core with time.
If you want different image upload functionality then best thing is probably to write your own and not to rely on the core to supply working GUI for it.