Google Wallet not working.
Lack of multi windows.
The pen feels a bit cheap still (loved the feel of the Palm Tungsten metal ones that were telescopic). Though fixable as I think I'll get a dual use pen/pointer to keep in pocket/briefcase, I'm a fairly large bloke too, so having that larger pen will help too, this current one isn't really of a decent size/thickness/weight to use for long periods of time, I think my hand would 'claw' up.
Lack of cases for a while (the official 'flap' one is good, got it at last but was making me twitchy not having it protected. Wish there was a good/cheap pouch type case to slide it in for extra protection). And/or the 'flap' phone case, the front of it, the actual flap, is wonderful to touch, but the back is the same uber slippery plastic that the default one is. Can NFC not be done through a very slightly thicker case with a built in rubberised coasting, as the Nexus7 has? This thing is still very, very slick, and I can see with slightly sweaty hands, I'll need to be extra careful.
The built in Samsung Keyboard (that is SO incredibly good with the Swype/cool T9 like swype functionalty/left/right handed), but doesn't scale to other resolutions if you tweak the lcd dpi. REALLY a great keyboard, please make it scale! No, best keyboard I've ever used, and it's keeping me from tweaking the dpi.
The knowledge that when I do inevitably flash CM on this, I'll probably end up losing TMobile wifi calling, that for me, is working wonderfully.
Touch wiz is mildly... odd. But not as bad as seen before, JB's ability to disable things is really helping. But what annoys me somewhat is the different functionality for no other reason than to do it different it appears, and needing a few extra apps (like the photo editor) downloaded when built in apps rely on it.
Oh, no 32mb NII's in TMobile, and so much of the 16GB filled with Bloatware (steady Cyanogenmod, steady... your day will come).
So, all pretty minor (hopefully constructive) criticisms. Overall, still mad impressed with this phone. All phones should have the option to have it work with a stylus as well integrated as this.
If I had the chance to order things to be fixed;
Wifi Calling for Tmobile as an installable app so I'd be less twitchy about flashing with other roms.
Rubberised back.