I have a 200Amp/2Pole, 208V, service entrance rated switch, 25kVA, 240/120V, single phase transformer feeding a 100amp, 120/240V, single phase, 3 wire panel.
What size primary, secondary I need? Also secondary side transformer grounding size?
Keep in mind you have to look at Art 450 to protect the transformer and Art 240 to protect the conductors.
With secondary protection at 125%, which you 100 amp panel more than meets, you are allowed to go 250% on your primary protection so your 200 amp 208v switch is fine.
Your primary current, with no adjustments, unless I made a math mistake is 120 amps. However, you must protect the conductors at their ampacity, so if you are going to fuse your 208 switch at 200 amps, the conductor must be rated at 200 amps, most likely a 3/0 Cu. and the 200 amp fuse would require a #6 ground.
The 3 #1s for the secondary to the 100 amp panel is actually over kill. #3 would normally be sufficient. If you were using #3, your system jumper (ground) could be a #8
Keep in mind your secondary conductors must comply with 240.21(C) as far as lenght.