The fronts had twin 36.5mm pistons regardless of year, but the Gen3s were spaced out farther (114.5mm vs 107.9mm) so they had more leverage on the disk. That means greater braking force for the same pedal pressure, which is why they went up with the master cylinder size.
Rears went up slightly in both piston size and spacing, which kinda counteracts each other. Static front to rear ratio went from 60% Front (Gen2) to 58% Front (Gen3). I'm 99% sure they both use the same proportioning valve, which is pretty close to ideal for street tyres.
I've got a whole spreadsheet calculating all the ratios and weight transfer, etc, but in the end it pretty much came out that Toyota we're spot on with what they came up with (who'd have guessed :D)
As for master cylinders, most reports say that with Gen3 brakes, a 7/8" is decent but with longer travel, 15/16" is a good middle ground, and that a 1" gives great feel but with a fair amount of effort.