Answered[ Edited ]
I have seen it in stores, yes, but if it's a trip for you to get there, I would call ahead of time to be sure that they have it in stock. I also really like both of them, to be honest -- they are different enough (but not so different that you "need" both unless you really love the colors). If I had to choose, I think I still prefer the first one, but there are shades that I love in Naked 2, too. (I'm fair / cool-ish / dark haired / blue eyed, for reference, and both work on me.)
They are both still available in stores. I just bought the first Naked palette yesterday. The colours in the first palette are more vibrant and the colours in the second palette are more sheer, at least that's what the Sephora sales rep said. I think the colours in the first palette are more different from each other than the second palette, if that makes sense. The second palette looks more neutral and I can understand why the sales rep recommended the first palette. I guess it really depends on what you're looking for.
The original Naked Palette (and the Naked 2) are part of Urban Decay's permanent collection, so they will be around for a while . I find that most people prefer the Naked 2 if they have a fair complexion with rosy undertones, where as individuals with yellow complexions with medium to darker skin tend to prefer the original Naked palette. However you can wear either palette and still look fabulous!
The Naked 1 is almost always available at my local Sephora store, though if you had your heart set on it, call ahead. The Naked 2 isn't currently in stock there, though they said they were expecting some soon.
I have cool skintones and like the Naked 2 better. It has more of the lighter colors that I find more useful to me, some of the darker ones in Naked 1 I can only use for night looks, they are a bit much for a work environment.
I researched both of them, and after Christmas I went with the first Naked. I recently saw the second one in stores, and I am so glad I went with the first one. I wear different combinations with all the shades. I have light skin that tans easily in Spring and Summer, greenish eyes, and brown hair if that helps any.
Sephora carries both Naked 1 and 2. At my locations it is always sold out or not in yet but you can always order it online and Ulta does a much better job of keeping things in stock so if you're out of luck at Sephora go there. I dont own any of the palettes but after playing with the testers several times I decided that I like Naked 2 better(Right now I have fair winter skin, light brown hair, brown eyes). Naked 1 has too many darker/smokey eye colors in it and Naked 2 is almost all neutral colors that I can wear everyday.
Right now I'm working on putting a good dent in the neutral colors I already own before I get Naked 2.