I'd be okay with Genesis being like a secret boss we can find hidden away in a cave. Literally just a boss encounter with no impact on the story - that would be fine by me.
This is the only acceptable way, tucked away in a corner and largely unnoticed.
This actually made me think how hilarious it ould be if Ansem returned the favor and was a secret boss in a later part. But some might get pissed that hes even in.