I forsee 1 or two team members being revealed as Hydra, as well as at least 1 of their allies (not counting Sitwell, the bastard!) and basically The Bus Team falling back, fortifying themselves, and straightening up their own mess.
Meanwhile, SHIELD and HYDRA's dirty laundry went public. But, there is still a need for SHIELD, and so I suspect we will see a very clandestine, very shadow version of SHIELD, with the AoS team being at the forefront.
With HYDRA brought into the modern day, the team now has a central adversary to chase. Centipede will be revealed as a HYDRA project, thereby opening a proverbial can of worms for the team to start dealing with.
With both Hill and Fury off the SHIELD beat, that pretty much leaves Coulson holding the SHIELD reins as far as I am concerned, and we're gonna see Coulson step up to the plate in the way that Maria Hill SHOULD HAVE in the absence of Fury.