I realize you would have had to retcon the timeline utterly, but...
I would have had Atari stick MARIA (for the extra sprites, extra compatible colors, and bitmap field), FREDDIE (so that mapper chips become unnecessary when games inevitably grow beyond 64K), POKEY (for the extra sound channels, and so that Atari can use the SIO Bus to interface a floppy drive of Atari's own design), and SLAPSTIC (so that they can control their own market lockout), and possibly license the 65C02 core to clock it at 5.35 MHz (to get the most out of both MARIA and the Picture Processor, at the same time).
I might also adopt the "Famiclone" method using the CX-9 joystick jack, but using Nintendo's timer-strobe-output method of button registration for the digital pins, as this leaves open the possibility for analog input controllers for driving and isometric games.
Nintendo can always put the extra chips on the Disc System, then add them onto a hypothetical backward compatible Famicom II in 1987, just in time to ruin the PC Engine's value proposition...
Did some ninja edits.