Utopia/Banks big focus is on internal empire dynamics. I fully expect the next two updates/expansions to focus on external (non-combat) empire dynamics and warfare, in either order. The former would hit things like an expanded diplomatic system, expanded federation mechanics, possibly other alliance systems, etc. I would also hope that some form of interstellar trade system would fit in there. The latter would hit on combat rebalance, some sort of fix to doomstacks, actually usable military stations, revamped ground combat, perhaps doomsday and planet destroying weapons, etc. I could also see some form of espionage mechanics fitting into either one of those. Of course those are just core ideas, each one would also include all sorts of things I can't even imagine at the moment. Really not sure which one I'd like to see first.
Three big patches/expansions, covering the three core areas of Stellaris gameplay. With that, I'd consider the 'core' game fully finished and fleshed-out. Looking really long-term I'd then hope to see a focus on more events and other dynamic content, especially mid- and late-game ones. Second round of anomalies, more colony events, new end-game crises, etc.