One thing I noticed is that Shadows is much more... unfocused. There are a ton of quests all over the board, and the players are going to be split up doing various things the whole time. They're not much interacting with each other, just responding to the general board conditions and their own quests.
In Battlestar, you still have multiple threats (4 dials, 3 kinds of Cylon ships, Cylon boarders) but it seems like you're all working together more against these threats. Perhaps it's the fact that the roles (Political/Military/Pilot) make it clear that each person is most useful in one area (whereas in Shadows it feels like any character can do any quest, mostly).
Most of all, though, the fact that all players are actively involved in every skill check that happens gives Battlestar much more interaction - there's more opportunity to really sabotage, but more opportunity to be exposed, and the Brig offers a way to "hedge your bets" and contain someone you suspect to be a traitor.
I also really like the second round (Sleeper Agent phase) in Battlestar, where some players may discover they're a traitor after all. This means nobody's past behavior can totally prove anything, and that in the first round nobody really wants to do TOO well as a human, lest they turn out Cylon and be hopelessly behind.
When Jeff declined to help us pass that skill check, was he really out of green cards? Or is he a Cylon? OR is he a human, but afraid he'll end up Cylon and lose to the humans?