This assumes that the ATCU is the stronger party, which I don't buy.
For one Coulson was able to get a Helicarrier up and running in secret, had the Bus 2.0 built, a fleet of quinjets he keeps fueled plus an aircraft carrier, according to last season several shell companies to generate cash with, and the ability to hack the freaking Whitehouse in a few minutes just to get in touch with someone, knows how to disappear rather quickly, at lest two superhumans on the payroll, tolerance of the last guy sent after him, global reach, and SHIELD knoiws what the fuck its doing.
The ATCU has support of the US government going for it but as such is likely only limited to within the US, can't catch crap on their own, don't have the foggiest idea wht they are doing since its pretty much established that they are increasing the levels of clusterfuck their ops devolve into, and are outmatched tech wise by SHIELD.
For pete's sake the ATCU's first appearance involved getting schooled by three SHIELD agents and Coulson getting a picture of Price letting him get info on her when the ATCU was still supposed to be a secret organization.
To me, it's a separate issue. The question isn't whether SHIELD could win in a fight, it's whether the bad guys would get away while SHIELD is fighting the ATCU.
Except the ATCU isn't just focusing on bad guys, they seem to go after anyone with super powers like the gestapo.
Seriously if this were an X-men tv series the ATCU would be the bad guys.
Should Coulson really be helping people like that?