For some perspective, CD trays, like the PS2 and Xbox had, that retracted mechanically were viewed as sleek and futuristic, and that's why slot loaders like the Wii and PS3 gained traction too.

It was an aesthetic choice, like the move from green LEDs to blue, though that has historic significant as blue LEDs are a relatively recent invention as the were incredibly difficult to figure out, so blue LEDs were seen as futuristic and opulent and used in everything consumer electronics for a while.

The PS2 slim has a CD flap, that might be the last console to have one

There's also whatever is going on with the PS3 super slim but I think that is in a category of its own

Cost. I think all of the 5th generation were top loaders. On the cd audio side nice stackable separates were tray or slot. Cheap stand-alones were top.

6th was a split but then I think the perception of slot or tray loading being more prestigious moved everyone to slot/tray.

Plus I think top loaders might have been less secure. I certainly remember a number of physical mods or swap techniques that defeated top loader security very easily.

Same thing happened with videos as well. Started with manual top loaders and then moved to slot.

The original Xbox had a tray because it was basically a PC, and had a standard IDE CD-ROM with some minor changes. They weren't standing apart, they were following the new standard of the time, PCs, and it was probably more to do with cost savings by using common parts. They also had a standard IDE HDD. Even their weird proprietary controller port they used on the original Xbox is just USB! Its the same wires, they just screwed up the pinout. you can replace one of those weird controller ports with a normal female USB and then plug all sorts of USB devices into the Xbox and they just work.

I only single out the Xbox because I've taken them apart, I imagine the PS2 is similar. At least PS2 didn't intentionally mess up their USB ports.