XO of SR2

I would actually assume it would be Joker. Assuming this isn't a conflict within the established chain of command system they use. Though both Traynor and EDI function closer to what a real XO would do. But neither of them are official Alliance soldiers to have that position.

space hamster

since its a human ship, it would be Ashley/Kaidan. If they aren't onboard, I would say Adams.

Adams would be a logical choice as a senior officer with a long service record. Being chief engineer as well is not a problem, Pressly was both chief navigator and XO, if I recall correctly?

James' rank is ambiguous; he's consistently referred to as a lieutenant in ME3, though ought to be higher ranked than that if Paragon Lost is canon (he gets a promotion at the end, if memory serves). Either way, having both the captain and XO routinely absent away on field missions is probably not a good thing (even if it did work for Kirk and Spock )

Who was in charge when they were away?  McCoy or Scotty?  

Considering the situation the Normandy departed from Earth, it could be that the planned XO was never aboard. After all the planned CO was Anderson, and he chose to stay behind. Perhaps Anderson even planned for Shepard to be his XO like in the beginning of ME1, but never got to telling Shepard that.

Further strengthening my argument that Normandy in ME3 simply has no appointed XO.  It's not Adams or Adams would be there in all cases since he doesn't leave the ship.

If there were an appointed XO, the order to still likely have been verified by the XO; and, at any rate, no one other than the XO would be telling Joker to leave in any other instance... and that person changes around... it can be Garrus or even Samantha, depending on Shepard's LI.  We are told right at the outset that Normandy left earth with a bunch of people onboard only to oversee retrofits... no XO and Shepard never appears to acquire an XO at any point afterwards.

The only other possibility is that Ashley or Kaidan are meant to have been Anderson's XO and so arbitrarily become Shepard's XO after Anderson clearly transfer command to Shepard.  Therefore, Shepard's XO is in the hospital for the first part of the game and he/she is left running without one.  If shot, then Shepard shoots his/her XO and again, runs without one for the rest of the game.

If that's the case then, I don't understand why there is no dialogue with either Ashley or Kaidan about them re-accepting the position of XO on the ship when Shepard approaches them to rejoin the crew.

The Normandy is an Alliance military vessel, so the XO couldn't be any of the aliens. They're passengers and not part of the official chain of command.

The XO is probably the Virmire Survivor, since Ashley and Kaidan are the senior Alliance military officers on board after Shepard. If the VS is hospitalized, dead, or assigned to the Crucible, my guess would be that Adams is probably the XO. Chakwas outranks him but she's a medical officer, and medical officers don't command warships (they're specialized entirely in the medical field). Adams seems older than Joker, and might have more time in service / grade.

Adams would certainly be a more believable XO than Joker at least. Adams has the bearing of someone who would be fit for command. Joker doesn't. He might be a good pilot, but he's also a bit immature and lacking in military bearing.

This is the first time I've ever read a post from someone saying that. She has always remained behind Joker not saying anything
Have you not taken your LI on the beam run?

Between Kaidan and Adams. Maybe James if he's up for it as I dont feel Ash is experienced enough even with her new rank.

EDI and the guy who kept walking around the mess hall make a better contender than any of the aliens.

I do understand the purpose of an XO and that IRL there would always be one... However, as themikefest continually says... this Alliance is not a real military, they can do whatever they like.  Some people took issue with Miranda arbitrarily being Shepard's "second in command" so I'm inclined to believe that it was intentionally left out to enable different players to head canon in whoever they felt most appropriate for the position... i.e. to enable, if the player wished, to imagine Shepard passing off the conn to an alien if he/she desired.  I don't object to anyone considering Adams as XO, I just wouldn't go so far as to say that anyone who wanted to put, say, Garrus, into that role would be totally wrong to do so.  Shepard is a spectre; the ship is only "somewhat" Alliance; so Shepard could, I think, take some liberties with how he/she manages the chain of command under him/her.  IRL, a commander would not be able to just go around adding "aliens" to his/her crew either; and Shepard does that through all three games.

The bottom line here is that the fact remains that Bioware did not specify an XO in ME3.  They did in both ME1 and, in principle, also in ME2.

... which the whole fraternization thing was pointless wasn't it?  Shepard could fraternize and there was never any action taken by the Alliance.  If the fraternization occurred with the VS, the VS even received a promotion.

I'm fine with the "what if's"... In fact, I've think I've put in various "arguments" here for a number of different choices as XO.

1) Argument for VS - that they were intended to be Anderson's XO (hence, why it was that Anderson contacted them to get to the Normandy to escape earth).

2) Argument for Liara - that she occupies the former XO's space on the ship

3) Argument for Adams - that he is Chief Engineer and that the entire crew is basically engineers overseeing retrofits.

4) Argument for Garrus and other - that he is frequently seen giving Joker the direction to leave the commander behind. (Additional argument - Turian generals salute the man and he/she may be next in line for becoming Primarch and Normandy is a co-design between the Turians and the Alliance.)

5) Argument for Joker - that Shepard effectively tells him to look after the ship when leaving for the Chronos mission.  (Additional argument - It is usually Joker that Shepard communicates with over comms... e.g. Just before the final battle when Joker tells Shepard "I'll hold you to that.")