I decided to start a new save and forgo the new expedition feature in the Anomaly. I feel like part of the fun is starting from scratch and finding shortcuts to get units, complete milestones, etc. Plus I often play my expedition saves even after the expedition is over.
I made it to Phase 3 before I quit playing today. Overall I like the expedition. Nothing has been particularly annoying but I guess that could change in the next phases.
How's it going for everyone else?
I think you made the right call. I DID use the Anomaly expedition feature and loaded up with elements and tech I thought might be useful, but none of that was available when the expedition started; even when I got off planet, calling the Anomaly wasn't immediately an option. I'm only a few milestones in, I'm sure I'll see it any minute now, but if I'd thought it through I might have stored more mid-game materials! I'll update when I get there; very curious about what else I can bring over from my main save.