Agents of SHIELD Season 2 has Phil Coulson where he should be: Director of SHIELD.
Just one GIANT-MAN sized problem: Nick Fury likely did not have any legal right to make such a promotion. No amount of Pym-particles could shirk the fact SHIELD had been disbanded, with its members either wanted for questioning or subject to arrest warrants for treason. Never mind the fact the world also thinks Fury is dead.
While the exact organizational structure has not been stated, SHIELD operated as a branch of the US military (as evident from the questioning by the Joint Chiefs at Congress at the end of Winter Soldier), with also an international oversight committee empowered to make policy. SHIELD was headed by Secretary Alexander Pierce (who likely was confirmed by the US Senate), run by Nick Fury as Director (also likely confirmed by the Senate), and headquartered in Washington, DC. In the wreckage of Winter Soldier, SHIELD was disbanded and political fallout for the fictional US President was overheard on talk radio in Agents of SHIELD.
Did Nick Fury have any legal right to appoint Coulson as Director? It is extremely difficult to envision any statutory authority to do so. However, Fury arguably had apparent authority from a Realpolitik point of view: Fury had all the secrets to rebuild the organization. As such, giving those secrets to Coulson effectively is only enabling vigilantism that borders on treason, albeit justified by the necessity defense.
There is a small amount of evidence that Coulson’s appointment is operating under limited government approval: at the end of Season 1, the former SHIELD agents were not arrested with the HYDRA agents, surgically altered soldiers, and Cybertek employees. Either the arresting agencies decided to ignore Coulson’s team or give him tacit approval by not prosecuting them for attacking General Glenn Talbot and other US soldiers in Canada. The US Government still needs SHIELD to combat threats such as HYDRA, thus might be operating with plausible deniability of Neo-SHIELD’s actions.
We will know for sure as Season 2 unfolds.