I wouldn't mind having some shards in friendly territory, and some not. At least that way we have options for variety. Either classic retrieval by flying it back, or just having it spawn in your territory (maybe in this case you get a bit more firepower in the exo waves) or building a teleporter while under fire. As long as it varies each time from the last time, I think that would go a ways towards fixing the feeling of exhaustion that repeated retrievals bring. Fallen Spire is more narrative than the usual AIW game, so you might steal some pacing techniques from the world of novelists. Rising action, climax, brief downtime, then a new rising action and so on.
Also a question, when the shard is retrieving now, where are the AI forces focusing? It doesn't seem like they're after the shard that much now, they just seem to go after everything. I think I even had some exo waves fly right past it, only taking pot-shots, and then go on toward my homeworld.
And a note, without spoiling anything, now that I'm getting deeper into the campaign, the back-story that is being revealed by the journals is getting quite good. I actually got a little chill from one of them. Good work!