Is it mostly a destruction issue with the Nidoking? I can see how it might be, since ground type moves on a train are... not the best combo, in which case I suspect an Excadrill (which are tiny) would probably not be permissible either.

How about a Haunter? They're bigger than Nidokings at 5'3'', but since they're made of gas, I'm not sure if size is an issue. If that's still too big, I can just shoot for his Toxicroak.