Do you just mean via injection into the N64 Wii Virtual Console emulators? I've never found those to be very useful. I tried to figure it out once, but didn't really get anywhere. From what I can recall, these were the issues I encountered: I couldn't find a romc type 2 compressor, which is the type with the highest compression ratio, and how the Super Smash Bros. emulator's ROM is compressed. Since an injected ROM cannot be larger than the original ROM, there is therefore no way to inject a modified Super Smash Bros. ROM into the Wii Virtual Console Super Smash Bros. emulator. You could inject it into a Wii Virtual Console emulator with a larger ROM file (the Sin and Punishment emulator is a popular choice, with a 256 megabit base ROM), but then you run into issues with emulator differences. The emulation varies significantly between the different Virtual Console titles, due to usage of various game-specific "hacks", and different hardcoded control schemes. With the Sin and Punishment emulator, for example, the magnifying glasses are surrounded by a black box, and R / Z are mapped to R / L instead of Z / R respectively.
In contrast, the Wii U N64 Virtual Console emulators have no weird ROM compression or filesize limit for injected ROMs, have fully customizable controls, and have game-specific configuration files for implementing game-specific "hacks". In fact, the reason that Super Smash Bros. can be injected so well is because Nintendo was nice enough to include a bunch of unused/unfinished configuration files in the Virtual Console downloads, including one for "SmashBrothers JP"! (Several other gems are in there, including "Banjo2", "GoldenEye", "BioHazard2", "Perfect Dark", and "pokermon snap".)
By the way, the analogue stick issue with Hid-to-VPAD that I mentioned earlier can apparently be circumvented by
changing the game configuration in the emulator.