I also know how it could be done...
Delve into the more tragic element of Flowey's backstory (I won't say what his backstory is, so that the game isn't spoiled for anyone)
Make sure he stays a villain. A villain can be a protagonist, too. After all, the protagonist is just the main character in a story, a protagonist doesn't have to be pure-hearted.
Switch up the normal Undertale combat system to support Flowey's friendliness pellets, among other attacks.
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