My assumption is that Microchip has a large customer who is demanding as perfect of a match to some 20+ year old design, and Microchip is more than happy to produce this ancient design for them.
ARM926EJ-S gives us a big hint: J for Jazelle. If some customer has some old Embedded Jazelle/Java code that they haven't bothered to update in the last 20 years, perhaps its easier for Microchip to just keep making ARM926EJ-S rather than forcing them to upgrade to Cortex-A5 or A7 (which although newer... these newer chips have all gotten rid of Jazelle / hardware execution of Java code).
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Code-wise, there's probably a lot of downsides. But electrically speaking, the SAM9X60 is an extremely well designed BGA with well-matched VCC/GND pins that has a 4-layer reference design. (Or at least: the SiP version SAM9X60-D1G)
Designing an 14mm x 14mm BGA223 that can be routed on a 4-layer board is no small feat. And therefore, this is probably one of the easiest BGAs to layout for a beginner, and lowers your PCB production costs.