In hardware, only Denise would have to be changed. In software all graphics related stuff would need to be rewritten (graphics.library, intuition.library?, application code banging the hardware). This is also necessary for RTG cards (most use chunky modes, too). The only way to go compatible is to add chunky modes and keep the planar ones. (IMHO missing this opportunity on the AGA chipset was a big mistake; software support could've been added later.)
OTOH, adding an RTG card takes care of the same problem, usually adds a lot of 'chip' RAM and allows for faster processing. So if you're not talking about recreating the Amiga and adding chunky modes en passant (e.g. Minimig), the RTG path would be the smarter one.