Every emulator should have most of these input-related features but I haven't found anything with more than a small fraction:
Default and custom input profiles. Custom profiles can have game-specific input bindings. Bindings in custom profiles set to the 'default' value defer to the binding in the default profile; it's important that custom profiles aren't just initialized as a copy of the then-current default profile as this makes it impossible to later change some non-overridden binding in the default profile and have it automatically propagate to existing custom profiles.
The emulator should remember which custom profile was last used for which game, based on the ROM hash or filename. (The emulator should also automatically save any relevant per-game emulator settings, but I think you want that separate from input profiles. As an example of what not to do, if I set the CPU overclocking for Metal Slug in MAME to 200% to