A big plot point was that McDuff's folks didn't know how to build weapons like those aboard the Enterprise. So it might have been a capital mistake for McDuff to pretend to be the skipper of the starship when he didn't know the first thing about how the ship worked. By pretending to be the XO, he would have some authority to make the heroes believe they had a mission, but he wouldn't have to get too entangled with actually conducting that mission.
(Actually, the XO would probably have more difficulty hiding his incompetence than the CO, as the executive-wannabe would have to micromanage the advanced alien technologies to some extent. But perhaps he was aware of how Starfleet handled things? Unlike most real navies, Starfleet has the CO micromanage maneuvers and weapon operations and the like, while the XO mainly just repeats the CO's highly specific commands.)
As for the inability of the Satarrans to build photon torpedoes when they could build memory wipe weapons... Actually, that's more realistic than the rest of Star Trek where alien species have the exact same weapons capabilities as our heroes. Different paths of weapon evolution in different cultures are only to be expected, unless those cultures are at constant contact with each other. Of course, the Lysians were in contact with the Satarrans, and thus would have devised countermeasures to the memory weapon.
Timo Saloniemi