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Shortage of Retina-capable apps
Yes, the new Retina display looks terrific; however, there just aren't enough apps currently in the App Store to take advantage of the awesome resolution. Right now, Apple has a special section in the App Store that's dedicated to a whopping 42 apps for the new iPad -- most of which are unappealing to me, personally. As such, some of us early adopters of the new iPad are going to have to just wait it out while app developers upgrade currently-existing apps or develop new ones. I don't mind that, but just be aware that if you're looking to purchase the new iPad, there currently isn't a whole heck of a lot in the App Store that will allow you to take full advantage of the new Retina display.
See also: 10 stress-relieving apps for iPad
Still no external storage option
You know what would be amazing? The ability to import/export data to/from the new iPad via an SD or micro SD card. I can't imagine it would take much to fit such a feature into the form factor of the new iPad, and it would really make life easier for things like transporting pictures and video -- especially with the addition of the 5MP camera. Sorry, Apple, but iCloud and iTunes syncing every single time is going to get old; never mind scenarios where neither are an option and you want/need to share pics/video. Plus, such an addition could allow for someone to make more out of a filled-up 64GB new iPad.
Dictation instead of Siri
I find Apple's decision to include a quarter-hearted Siri -- which they call "Dictation" -- a bit odd. Honestly, if Apple expects me to use my iPad as a camera while I'm traveling or walking around with my family at a farmer's market (or wherever it is they show in their promo video), why wouldn't they just give me the complete package and include Siri -- especially if I have a 4G model? From the looks of things, dictation works similarly to Siri, in that it sends your voice input to Apple's servers. It's just such a strange "feature" to pare from Siri, I think.