**FULL SPOILERS AHEAD FOR CAPTAIN AMERICA: CIVIL WAR, AND AGENTS OF SHIELD**
Season 3 of Marvel's Agents of SHIELD certainly dropped a lot of the plot elements that came to define the show over its three year run. Ward is gone as is the threat of Hive. The team seems splintered and Coulson is no longer the Director of SHIELD.
This acts in many ways as a fresh start for the show; and there's many ways they can take the show. Below are my main two ideas for where they'll take the show in the upcoming fourth season.
Secret Avengers
At the top of my list is Secret Avengers. Now at the end of Season 3, we see that Dasy is on the outs with SHIELD/Coulson (which echoed the Cap/Tony relationship from
Captain America: Civil War). Now we know that Marvel was setting up Bobby and Hunter for their own spinoff series called
Marvel's Most Wanted, which while it failed, I think it's telling as to where Marvel wishes to take the series.
As it stands with the MCU as a whole, you have characters that are in opposition to SHIELD and the government, and just like the films, I think the TV show will keep these two ideological sides in mild opposition with eachother for some time (at least until Thanos shows up). So having Daisy head up a group of Secret Avengers would be a fun idea, and could open up the show for one off appearences from Cap's team of Avengers. It would make sense to have Jeremy Renner's Hawkeye or Paul Rudd's Ant-Man show up for an episode or two and while it might not be explicitly called 'Secret Avengers' I would be shocked if we didn't get some variation on this idea in some capacity, it's just that with the MCU film slate as full as it is, it would seem that outside possibilities in a few of the films (which even seem like a stretch), that Agents Of SHIELD seem like the best avenue for this.
A lot of people expect LMD's to play a big role but I think if it is going to play a role, they will be the antagonists. Having an LMD of a high ranking official pulling the strings could certainly call for Daisy and company to hide
(Pre) Secret Invasion
I mentioned this is in my Season 3 review of Agents of SHIELD that I think Marvel could start seeding for a potential Secret Invasion storyline as they have with the Inhumans. It adds a certain 'wow' factor to the show. Certainly with the show not being the ratings hit it was expected to be, Marvel and ABC are going to be looking for ways to entice the show for viewers on the fence or those who haven't watched the show; and I half expect the show to soft reboot itself next season but also include a major element from the comics, and the Skrulls/Secret Invasion simply make sense.
What's interesting is reading various fan fiction for Agents of SHIELD. many people seem to enjoy Coulson as a villain in some capacity. So having a Skrull impersonating Coulson could be a fun way to play with the expectations of this beloved character (like they did with Ward). The only reason I think they wouldn't do this is that they already played with a similar concepts with having Ward being posessed by Hive.
Kevin Feige has said the Skrulls are fair game for Marvel Studios, so I imagine the question at this point is 'when' not 'if'.
These are my thoughts on where Marvel could take Agents of SHIELD in Season 4. LEt me know in the comments what you'd like to see.