So, this contains spoilers from the show, you are advised citizen. So, i will show you some of my theories that i had before the show, and now they increase the chance to get them after the first 3 episodes. This is mostly because i am sure that we will get more than 1 season (maybe 4 like Rebels who knows).

1) Origin of the Deathtroopers: Some people (including myself) see some resemblance in Crosshair with the deathtroopers: His coldness, brutal executions, get the job done, no hesitation and more capable than a normal recluit. Crosshair could be the one who trained the first batch of deathtroopers (the armor looks similar). In an apart note, i really like to see humans using clone armor (nod to the dark horse vader comics that are really worthy).

2) Gideon and the Darktroopers: It makes huge sense that Dave starts putting some strings with his shows and connecting them all together. Gideon plays a key part in Filoni's plans ans seeing how he start his career in the Empire, and the early stages of the dark trooper project (with humans or clone bodies being used instead of fully droids).

3) SCAR Squadron: These guys in the comics were great, and they have a very resemblance with the Bad Batch (taking the name Task force 99, being brutal in their missions and bringing trouble to their enemies, different looks and abilities). I have a theory on how the Bad Batch could be them which i will mention in another point. 

4) More imperial officers appearances: With the changs that we are seeing between the goverment of the Republic and the Empire, we need to se some old faces really well known from the OT. My guesses could be a young Agent Kallus (and his training as an ISB agent), Yularen (we need to see his thoughts on the Empire, his change of attitude, forming the ISB), and more of Tarkin (his doctrine being the main message and law in the Empire). For Thrawn I think that it is too soon, but i will be down to see him later on. 

5) Change the Clone armor for Stormtrooper armor: So, in a moment of the series we will get this (mostly after a main incident on Kamino), how the remnants of the clones who are loyal to the Empire will start using Stormtrooper armor and mixing with the human recluits.

6) Clone rebellion: I will stop in this one, especially because of the stuff that they could make about this, and all the ways that a rebellion on Kamino could happen. First i will tell you how i see it (with a dark ending): The Bad Batch returns to Kamino, they must hurry in order to safe Crosshair from the Empire's wrath. Suddenly, they are surrounded by regs, Lama Su and Nala Se. We get the reveal of the true purpose of Omega. Hunter makes an inspirational speech to the other clones, than later on remove their inhibitor chip. The Empire is aware of this, so they send the best of the best to stop the rebellion before it is too late.

A lambda shuttle comes down, the lower door opens up to reveal either the 501st with full clone armor or the 501st with new stormtrooper armor; and their leader, a dark lord of the sith, with a personal task revolving the Bad Batch. A huge war like the one from the Clone Wars, but instead of droids we get Storms (humans and clones) vs Clones. Omega and Hunter will escape, and the rest of the Bad Batch will stay behind protecting their withdrawal. Echo 's fate will be seal in here, and the rest of the Bad Batch face Vader in a badass scene. Vader puts them down without killing them, and they get Crosshair's treatment (brain the inhibitor chip to make them fully loyal and become the SCAR Squadron). Other choices instead of Vader could be Delta Squad (wich i am down to see) and Boba (at this point i think that he is too young to do this).

Edit: After finishing The Imperial Handbook, i will post some interesting stuff about this.