I have created a hack of Mega Man Zero 3 in the Mega Man Zero/ZX Legacy Collection that effectively changes Zero into Omega. The premise is similar to the GBA ROM hacks done prior. Omega, the final boss, has three phases. The final phase is a mirror battle with stronger variants of Zero's attacks, several unique abilities, and minor design changes. Gameplay and a detailed list of changes can be found here: https://www.youtube.com/watch?v=P2fXjP3SZlI
The video also includes the enabling of oil splatters, which spawn from enemies destroyed with a non-Buster weapon, outside the Japanese version.