The Four goes all the way to Union Square. So does the FIve. And both run express in Brooklyn, so they should be faster to Atlantic Avenue than the Two or the Three, which both run local.
But sometimes the Four and the Five get really backed up in the morning, meaning that they run more slowly than either of the local trains. And if the departure board says that the next local train is arriving immediately, but the next express train isn't for another three minutes, then it can be worth it to get the local.
This is (a) especially true when it looks like the local has seats (there are almost never seats on the express) and (b) sometimes not true when it says that the express train is coming in two minutes. Sometimes, that two minutes evaporates almost immediately into zero minutes.
Once you're on the express or the local, the next decision point is at Atlantic Avenue. Almost no matter what, even if the ride has been smooth all the way to Atlantic on the local train -- even if you have a seat -- then what you want to do is get off at Atlantic, at which point you have to decide whether to get on the Q, which is in one direction, or the N or D in the other direction.
If you're on the express and it flew to Atlantic, then you might want to stay on the Four or Five all the way to Union Square. If you have a seat in an air-conditioned car and the train has been moving the whole way, then you're all set. Just stay on that train. If you're standing, then it's a bit of a tough call.
But if you can get cell service as you enter Atlantic Avenue, and your Google maps tell you that an N or a Q is coming in the next four minutes or so (meaning you can make a quick connection), then the best thing to do is absolutely to get off the express train and run to the N in one direction, or the Q in the other.
If you do decide to transfer, well, the game resets and new variables come into play. The Q is almost always really crowded by the time it gets to Atlantic. So if you take the Q, then you're likely going to be standing the rest of the way to Union Square. On the other hand, the Q comes reliably in the morning and doesn't share a track with anything else, so you know that if you get to the Q platform, it shouldn't be more than 6 minutes till the next train at most.
But on the N/D platform, you know that you'll be able to take whatever train comes. You have a higher probability of getting on a train quickly, and even of getting a seat on whatever train comes. But if it's a D, then you'll have a longer ride to 14th Street and a longer walk to the office on 16th Street.
If an N comes at Atlantic and there's a seat, and it arrives right as you're walking into the N/D platform, then you have won the golden ticket, my friend. It will take you the minimum amount of time to get to work. And you will have won that most meaningless of races.