I don't think you can really go wrong with any of those choices. Here's the thing. If you've waited this long to upgrade, I don't see any reason not to hold out until October/November (only 3-4 months away). By then, the Note 3, HTC's supposed competitor to Samsung's Note series, as well as the Optimus G2 should be out and available or on the verge of release.
At that time, there will probably be even better deals for upgrading to the Note 2, which would still be a "valid" choice, especially if you get a great deal for it.
My advice is wait, but if you can't hold out that long, then select purely based on your needs and the device that will suit you the best. If you want a big screen, would find the s-pen extremely useful, and don't mind the additional size, go with the Note 2. If you would prefer a more pocketable option, upgraded software options, and extra storage is important, go with the GS4. If you don't need that much storage space, prefer a very clean/nice form factor, and would rather have a metal build, go with the HTC One.
Based on the leaked images of the G2 (e.g. Optimus G2), that might be out much sooner than the Note 3 or the HTC competitor. Even with the oddly placed power button on the back and volume rocker, it still looks very nice.
