That said, if EV's are split by a state I would prefer the ME/NE system since it mirrors the weight of all states and districts in congress. I think there would be less chance of FL-type problems, since the most a recount could affect is one vote for a CD or 2 for the state.
In my view, you've identified one of the real positives that the ME/NE method produces - small impact of tightly contested EVs.
Unfortunately, the ME/NE method is fatally (in my view) flawed because of the horrorific problem of Congressional district gerrymandering. I would definitely NOT add to the importance of congressional district lines so long as they're drawn in such a blatantly partisan fashion.