I agree that NW and FF should have been skirmish game only. They just dont work as massed armies bases on the novel's and ruin any chance for a real war if the 5 kings campaign. they just never should fight anyone but themselves.
Yeah thematically, the Nights Watch shouldn't really be out fighting pitched battles against the various houses of Westeros. They never seemed to have the numbers for that in any case. However, there are probably hypothetical scenarios the players could come up with to justify (albeit loosely) why the NW and whoever are fighting each other in game. Perhaps the Nights Watch have a new high profile member deemed too dangerous by the opposing faction to be left alive, even though they took the black. So they come in force demanding that person be handed over, and the NW refuses. Or perhaps that force believes the Nights Watch betrayed the realm by sheltering/aiding the FF, and is now demanding its dissolution at the point of a sword. Idk, you could rationalize it somewhat, so it doesn't bother me. I mean Boltons units are showing up in everyone's army, and that actually annoys me more than NW taking the field. They did switch sides, but were never a fractured force of "neutral" mercenaries. I still hold they should be their own faction at this point, their units unavailable to other factions. But it's kind of too late for that now since everyone's been buying Bolton stuff. Wouldn't really be right to say "you can't use those anymore."
As for the FF, I have no issue with them being a playable army at all. If they're playing the NW, then that's a pretty thematic match-up. If they're not playing the NW, then perhaps assume the NW failed to defend the wall, and was destroyed, disbanded, or retreated from Castle Black. Mance's army is now on the loose south of the wall, and [insert house(s)] has formed an army to stop them.
My only issue with these two factions is that they were released before the Baratheons and Greyjoys. The intro page in the rulebook sets the stage for the war of 5 kings, so I figured they would work their way through those 5 kings/factions before hitting the factions on the fringes of/outside of that conflict. I find it hard to believe NW, FF, and Targaryens were released before Greyjoys. Speaking of, I think the Greyjoys are the ones who work the least as massed armies. They may be the most skirmishy of all. I don't recall them ever really fighting as anything other than raiders. But they're one of the great houses, and Balon is one of the five kings, so it has to be done. And I bet the models and rules will be really cool too.