Leaving it in the secondary will allow more sediment to settle out of the beer, but eventually this isn't going to matter too much. After a while your returns will diminish indefinitely, and with a stout I wouldn't worry about it as it isn't supposed to be a nice clear beer. If you wait a long time, like a matter months then the yeast will lose vitallity and it will take longer to carbonate in the bottle, but I wouldn't too much about a few weeks. I would just bottle it when you are ready and enjoy emptying those bottles that the stout is going to be in. In general, the secondary fermenter can hold a beer longer when you want it to clear up nicely, but with stouts and wheat beers especially, I just bottle when I'm ready and don't allow them to settle too much. I once got lazy and left a heffeweizen in the secondary for six months and it cleared up beautifully! It was so clear and golden it looked fantastic, however, it looked nothing like the heff I was going for. If you bottle your stout in the next couple of weeks I don't see any difference in the benefits of letting it sit in the secondary or the bottle.