Actually, now that I think about it, doesn't Kaiden (for those who didn't nuke him of course) now outrank Shepard? I wonder how that will be addressed.
Umm. He'll be higher in the Alliance hierarchy, but a Spectre Shepherd (assuming he wasn't stripped of that by the Council after the events of "Arrival") would still win.
The whole rank thing seems to be a case of Codex writers not knowing what story writers are doing and vice versa. At least as far as ME1 was concerned, it seemed pretty simple. You had your Marines with Marine ranks (Ashley and Kaiden) and you had Sheppard with his Naval Rank (Lt Commander). Both existed parallel with each other and the way the story went this seemed to be the case. After all, you had Ashley William's grandfather General Williams handling a Marine garrison at Shanxi. At the same time, you have Admirals commanding fleets (Admiral Hackett). The Codex writers on the other hand seemed to have been doing their own thing since (the internets tell me at least) that there is some BSG-esque combined rank system for the Alliance.
I find this retarded so I'm going to choose to ignore it
As such, in my mind Kaiden eventual got up to Major (feasible since he was a Lieutenant in ME1 and only 2 ranks away from Major) and is of equal rank to Sheppard.
It also makes sense in regards to Captain Anderson since the next step up from him would be Admiral and that's what he becomes.
Screw the Codex, it's just fucking shit up