Before it launched, the new model of the iPad generated a ton of speculation as to whether it would be called the iPad 3 or iPad HD. Turns out, Apple just called it "the new iPad". Original!
Short term, that may be a little confusing. Presumably, Apple will eventually quit calling this thing "the new iPad" and just refer to it as the iPad. And when it does, that's going to be kind of weird because Apple is still selling the iPad 2. (At least for now.) In six months, will you be choosing between an iPad and an iPad 2, with the iPad being the newer, better model? Do they just plan on calling it "new" until iPad 2 inventory runs dry? That's going to take some shaking out.
But long term, it makes sense. Think about the iPhone. The iPhone 4S is the fifth generation iPhone, which would make an iPhone 5, if there was to be one, the sixth generation iPhone. See? Confusing! Which is why folks are already predicting that the next iPhone will simply be called iPhone, and not iPhone 5. Simple.
And it's not like this is some major break, or a logistical nightmare. Apple tends to only release one major upgrade across its product lines per year, at roughly the same time, like clockwork. And until iPhone 4 and iPad 2, iPad products didn't have a version number. When they did, it got a little awkward. And why wouldn't it? Apple doesn't number anything else in its product line. You've got Macbook Airs, Apple TVs and a slew of other products that all get updated without changing the names.
You just want the new one.
You'll be able to tell which one is new because it costs more and has better specs.
And if you're buying used? You'll use a term like "third generation" or even the year it was released. In fact, I think a good analogue is to think of tech products, at least ones that get one update per year, like cars. You just buy the 2012 model, it doesn't need a version number.
The only reason this is at all weird is because of the iPad 2 and iPhone 4. Those were nomenclature mistakes. Ones that "New iPad" fixes.