I'm still sorting out all this transfer switch stuff myself, but I thought a generator transfer switch must be rated to handle your line service (which generally is 200 amps around here)--and by code the generator size is almost irrelevant. Please correct me if I am mistaken. I already have a Rink 100 amp transfer switch (donated by a family member) but my buddy who works for the power company told me the transfer switch had to at least match incoming service setup, which in our case is 200 amps...
Edit--A quick search turned this up:
http://www.steadypower.com/products...-(1Ph,-200A)&gclid=CNnFw5as5MMCFW0V7AodUjcA8w
This seems to be what I need., but still need to to a little more digging. For our MEP-004A I would specify the 25KW generator option to receive the correct item with a good margin allowance for amperage.
If you were going to split your 200 amp utility feed to two panels, one normal and one emergency, you could then use a switch rated for whatever the split was. So if you made your normal panel 150 amp, you'd make the emergency panel 50 amp, and you could use a 50 amp transfer switch to supply the emergency panel. The switch has to be rated for the highest service that may pass through it.
If your 200a utility line needs to feed the emergency panel full-rated service, then the switch must be 200a. But if you're de-rating to a lower capacity emergency panel (let's say 50a), you'd stick a 50a disconnect before the switch, then a 50a breaker before the panel (or as the panel main breaker). You could use a 100a panel, but you could not use a 100a breaker before it, and would have to keep all load breakers under 50amps.
A good thing to remember is that your protection devices, like breakers and disconnects, should get lower and lower or stay the same as they get closer and closer to the load. Your wire capacity can always be higher rated than spec, but safety devices should be the same or never lower than spec, and never lower than the one before it in supply.