If you already had a G-Note, I would say don't bother upgrading. The S3 may be the newest but, truthfully (at least in my humble opinion), it really doesn't have anything that is "Earth-shattering." As RaiderWill says above, soon enough most of the new S3 features will be hacked for the G-Note and most other phones. Just start browsing websites like XDA-Developers.
But I realize that that was not your question.
If you are looking for a totally new phone, then it is a tougher decision. Ultimately, I think the software advantages/disadvantages is a wash (excluding the S-Pen related stuff but more on that below) but the hardware of the S3 is, all-in-all, better. I like the screen of the G-Note better but the S3 should have a higher dpi and some may prefer that. Plus, while some may think the G-Note is too large, after playing with it a bit, many may find anything less than a 5.3-inch screen to be too small. The real advantage of the S3 is an A15-generation dual-core processor and (rumored) 2 GBytes of RAM for the US model. Even I confess that it's tempting but is it enough?
The real differentiator, and the reason I would go for the G-Note, is the S-Pen. There is (probably) nothing like it on the market: but the reason I say "probably" is that the S3 will come with an accessory called the C-Pen. I honestly don't know but if the C-Pen will have the functionality of the S-Pen, then it might not be long before the S3 gets at least some of the handwriting and drawing capacity of the G-Note. But that's a big "if".
Me, I'd go with the G-Note but you really can't go wrong with either phone.