Commodore owns the C65 IP. I don't think that they would even try to integrate the Mega-65 into the product line. Instead, I would expect them to move forward with the C65 as designed by Commodore and release it with modern options.
This would likely render the Mega65 and the C65 as different machines. As much as people think the two are the same, the MBA in me says it won't likely happen. The only reason that the Ultimate happened was the benefit for both parties and Gideon sticking to the origional roms and keeping the core system a C64.
That is not the case with the Mega-65. From what information is available, Mega-65 software won't run on an origional C65. Maybe Commodore will decide to run the C65 on completely different hardware. The Mega 65 is certainly out of the sweetspot for most Commodore fans, even though a Mister can be purchased for less than $200 USD. The mister can run far more complex cores than the the C65 and the Mega-65.
My best guess is that Commodore will go back to the well and design a C65 based on the origional specs. The could also add a C64 core instead of the C65 compatibility mode as well. Finally add an IDE to pimp C64 games to be upgraded on the C65 with better graphics and sound.
This would create a new eco system that would eventually spawn new software as well. Giving Commodore a future. Something they currently lack. With a logo like "8 Bits is enough" they could create a realm that nobody would or could compete with. With enahanced CPU speeds, new or upgraded software could demonstrate that the classics can truely attract both old and new fans.