To my mind, the challenge for next season of AoS will not be in coming up with interesting ideas (they have a slew of them, and let me say that, at this moment, I am deeply in the "Inhuman" camp for a whole range of reasons), but in maintaining the pacing and characters in a way that works (i.e., not like they did for the first 14-15 episodes this season).
AoS has done best with continuing storylines and villains, moving from episode to next. When they've done one-off "monster / super-villain of the week" tales they've usually been uninteresting, since there's just not time to do much with character, and their FX budget appears to be fairly limited.
That latter point is important — even with continuing characters, AoS needs to step up the unusual, to maintain that Marvel Universe feel. One early criticism of AoS was that it felt too much like a typical procedural; the minimal FX contribute to that, even if they fly on a cool, if improbable, jet.
Anyway, I'm eager for the return in the fall of AoS — with the "Agent Carter" mini-series helping fill the gap, along with the Guardians of the Galaxy movie (which should pump up some of the alien side of the MCU in a way that I suspect will impact AoS directly).
13 Big Questions For The Future of ‘Agents of S.H.I.E.L.D.’
With season 1 of Marvel’s ‘Agents of S.HI.E.L.D.’ now complete, we take a look at some new mysteries and answer some old questions.