Some Anvils Need to Be Dropped: Gaeriel follows a religion called the Cosmic Balance, which believes in balance in all things. When you suffer, an unknown other in the galaxy is elevated, and vice versa. One aspect of her religion teaches that Jedi are abhorrent, as they accumulate massive personal power, weakening their unknown counterparts. She even wonders, briefly, if Luke could be so powerful that the Cosmos had to send in the Ssi-Ruuk, reducing hundreds of sentients to mere droid batteries, to balance his power. Gaeriel's good friend Eppie Belden suffers from very severe dementia, and Luke, upon meeting her, realizes that this is not a natural result of old age for her, and that Eppie has untapped Force potential of her own. He shows her how to use a Jedi healing trance, and a few days later, Eppie is back to her old, fiery, lucid self. Gaeriel tries to explain that Luke is "dangerous, one of them, to which Eppie scoffs, and replies "Our teachers have taught us a lot of wisdom down the years, but also a load of guff." A most succinct criticism (notably, not condemnation) of religion in general, and religious intolerance in particular.
Tear Jerker: The entire last chapter, basically. Dev dies, but finally cleansed of Ssi-Ruuvi taint, having focused on healing his spirit instead of his body. Luke feels him Ascend to a Higher Plane of Existence through the Force. Gaeriel comforts Luke over the loss, but then the two part ways, Gaeriel feeling her place is to stay with Bakura, and Luke is (naturally) needed elsewhere.
What Happened to the Mouse?: The Ssi-Ruuk are beaten back from Bakura, but this was only one of their fleets, they're still out there, still aware of the galaxy at large, and the deal Palpatine made with them to keep them out of the galaxy is still void (since Palpatine is, you know, dead). They are never heard from again until very late in the New Jedi Order series.