The XO in 1 is Pressley and I don't think anyone can say different. The ship is alliance and he, Kidan, Joker, and perhaps Adams are all LT's but serving in different departments. With Kidan leading the marines and Joker the flight department Pressley is the one with experince in ship operartions and avible whenver you step off the ship.
In 2 it is Miranda. It is a Cerberus ship and she was assigned by Cerberus. Not only that she has experince in overseeing different departments and keeping them pointed towards a goal from her time incharge of project Lazzerus, which is more then anyone else on the crew. And it certinly dosen't hurt that she is bit of hard ass on the crew which makes my captain, Shepard, seem much more human and worthy of loyalty when he goes around the ship checking in with the crew and listing to what they say. It's an old trope really, the sympathitic captain looking out for the crew and the hard ass XO enforcing discipline and overseeing day to day operations.
In 3 it is much harder. Kiaden is promoted to Major and leading a ground unit and not there for much of the opening of the game. Ashley has no bussnies being an LC and I have no idea how she got promoted from operations cheif to lieutant commander in 3-6 months so I would never leave her in charge, certinaly dosen't help she isn't around for much of the opening either. Joker is again bound to the cockpit which prevents him from overseeing others. Adams would be a good choice but he is need in a woefully understaffed enginering. Vega is a marine with limited knowledge of ship operations and so not suited. I have to go with Cortez, he is familer with ship operations and incharge of a non critical department in the flight deck so he can leave it if need be. Only problem is he inssint on flying me everywhere so that leaves either Adams or Joker as the second officer in charge until he gets back.