It's simple really. It's all about the pen. Do you need a stylus or you're okay with your fingers?
Personally, I'm waiting for the Galaxy Note III with its own 1080p screen and maybe something closer to a six inch screen. After all, this is more of a table than a phone. And I'm going to buy it off contract (been saving up for a while now).
The reason is because I think Samsung has something really sweet going on there not its competitors, especially Apple who isn't too keen on because of past statements like Steve Jobs saying the stylus isn't for iOS. However, the market disagrees given that there are dozens of styluses available for both Android and iOS. I've got a couple that I use for drawing from time to time.
However, I only use the stylus for my iPad for specific tasks and I reckon that'll probably be the same for my future Note - only for some native Samsung apps like note-taking or drawing.
And given that the Galaxy S 4 is closer to being in the "here and now" than the Note III, which will launch in the fall, you have a choice to make. If you don't need a stylus, the S 4 is perfect for you. You also get the latest Galaxy smartphone. But you need a pen, you've got only the Note II unless, like me, you can wait a bit.
Also, keep in mind that while these two flagship devices may appear similar, one is still more of a traditional smartphone while the other really is a tablet. So, the choices are rather simply. Do you want to have a traditional smartphone or a small tablet with a pen. And there's nothing wrong with using a third-party stylus on your Galaxy S 4.