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BioShock 2 actually managed to do this really well when you inhabit the Little Sister. However in that case you are still the same character, but you are possesing someone else's body. So the awkwardness of controlling the new body makes sense narratively and doesn't really break the immersion.
Arkham City also does this well with Catwomen, but there you are controlling a character that essentially plays the same as Batman (aside from some of the things she can do.) But you can mostly get by with her by playing her much the way you would Batman. And then in regards narrative, her storyline is parrallel to Batman's which prevents any sort of immersion breaking narrative problems from arising."
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I think that the way I look at the final stranger mission is that those final missions at home with Jack, Jack sees his Dad as someone who did bad things and is now trying to get away from that and change himself. So regardless of how you, the player, see the John's death (whether it was sad or well deserved,) Jake would probably only see it as being undeserved since all he knows is that he did what the Feds wanted.
Thus it makes sense to me that Jake would be out for vengeance, but also what it does is if you played honorably with John it now opens the game up to let you do bad things. When playing with John I felt that I was staying with his character by doing honorable things, but as Jack I feel more open when playing to be a bit more of a jackass since he's willing to go through all the trouble to hunt down Ross.
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I meant to also make mention that I think depending on how you choose to go, dishonorable or honorable, that sort of determines how you will feel about the end of the last story mission. If honorable, sad; if dishonorable, perhaps that it was deserved. But I couldn't quite figure out where/how to work it in really."
