Well, I think one of two things has happened.
1. The most likely option. Katie Holmes gave birth to another man's (probably Chris Klein's) baby at a time when it would not be plausible to pass the baby off as Tom's. Just hypothetically, let's say three months earlier than the date released to the public. If this is true, then Tom and Katie would be forced to keep Suri hidden until the age difference would not be as noticable. There is a HUGE difference between say, a 3 month old and a 6 month old versus a 9 month old and a 12 month old. So I think we will see Suri when she is a little older. This theory would also account for the vastly differing sizes of Katie's belly in later months (prosthetic belly).
2. Not likely, IMO. Katie faked a pregnancy and they are trying to adopt an infant of the right age on the down low.