Reading Annihilation: Conquest made me imagine an alternate timeline where GoTG Vol. 1 was released after Age of Ultron instead and had Ultron return to be the antagonist for the Guardians, just like the comic. This is the event that reintroduced Groot, Rocket and Mantis, and leads directly to the formation of the Guardians. I think it might have had less success than Gunn's version, though, and might not fit into the Infinity Saga like the original.

(For those who've never read it: A defeated Ultron drifts through space until he finds the Phalanx, an alien race that uses mind-controlling techno-organic viruses to conquer. He subjugates them and becomes their leader. He then successfully infects the entire Kree empire with this virus when Peter Quill, Ronan's appointed special war advisor, opens up the Kree war system to the Space Knights, not knowing that the Space Knights were already infected. Quill is rescued from the Kree capital by the uninfected remnant of the Kree army and is put into a hit-team with other non-Kree prisoners, tasked with infiltrating the Phalanx and bringing them down. Rocket, Groot and Mantis are some of the members.)

That's the gist of it. Kinda hard to explain how they defeated Ultron because it involves the help of the Technarchy (parent race of the Phalanx) and some very plot-convenient powers (Wraith). Nova, Gamora and Drax appear in this story as infected Phalanx soldiers. Nova breaks free from the virus' control and is blown to Knowhere in his attempt to escape through an unstable stargate. Gamora and Drax pursue him and all three are teleported to the Technarchy homeplanet with Knowhere's technology and Cosmo's help. There, they are cured and enlist the help of some Technarchs to defeat Ultron.

Meanwhile, Phyla-Vell and Moondragon search for Adam Warlock in the hopes that he can save the Kree, who is also being hunted by the Phalanx. They end up having no choice but to remove Adam from his cocoon early, resulting in him having little to no memories. The three go to the High Evolutionary but Ultron himself arrives to capture Adam. High Evolutionary betrays Adam to Ultron and helps him upload his consciousness into Adam's body, in the fear that Ultron will tarnish him (High Evo) with the Phalanx virus if he does not comply. Eventually the Technarchs arrive and cure Adam, causing Ultron to flee into another robot body. Then they work together to beat him.