No. 1: Introduction Of The Secret Warriors
While there's no "Secret War" (at least not yet, as FOX still holds the rights to most of the intellectual property required - even following the flop that was Josh Trank's Fantastic Four), one of the most tantalizing teases that came at the end of SHIELD's stellar second season was Phil Coulson setting into motion a program recruiting powered people to form a new team; with Daisy Johnson/Skye as its leader.
The circumstances won't follow the exact narrative arc that saw this team's creation in the comics, but establishing a "secret" team of powered individuals gives the television side of the MCU it's own version of a strike team - like The Avengers only appropriately scaled down. After all, these powered people aren't just heroes; they're SHIELD agents. "Operating in the shadows" comes with the territory, giving the writers and showrunners a convenient excuse to play in the same sandbox as the film side of the MCU. There would also be ready explanations for the lack of regularly occurring straightforward crossovers and team-ups.