I don't have first hand experience so take this with a grain of salt but some that come to mind..
-less "prestige"/not as established yet
-since their just starting on their feet it is likely that they will run into problems in their program like scheduling and curriculum. Whether that affects your chances at a competitive residency is up for debate
-the quality of the rotation sites that are set up for you may be questionable
-no upperclassmen to give advice or shed some light on the do's and don'ts
I think there are definite advantages of going to a new school especially if you are the first class.. I just don't think those advantages have much to do with competitive residencies.