I think that Rush's visions/hallucinations of Gloria and Franklin are probably side-effects of his time spent in the chair, but that may be a far too logical explanation (given the stupid supernatural bullshit revolving around TJ it could, unfortunately, point to something else entirely). Rush might also be correct in his theory that the ship is trying to communicate with him.
Riley's death was quite effective (probably the best of the character deaths thus far) and I liked that Young and Scott were emotionally affected by it. On that note, hilariously, Chloe was even more superfluous in this episode than the prior one. Did she do anything in this episode other than comfort Scott at the end? They should just kill her off and give that pretty Lucian Alliance Redhead top-billing. She's a far more interesting and useful character than Chloe could ever be. Then again, Riley's rotting corpse is also a far more interesting and useful character than Chloe could ever be. And no, constantly making increasingly tenuous references to the aliens in the callbacks isn't going to help with that!
They solved the greater problems associated with the Lucian Alliance prisoners fairly quickly. I think that out of the ones they kept aboard Varro and Pretty Lucian Alliance Redhead (or PLAR. I'm trademarking that acronym post-haste) will earn their keep. Robert Knepper will obviously be the royal prick of the bunch, so there will still be opportunities for conflict.
Spoiler