No, this is upscaled, the 3D graphics are smooth on iPad not stretched. The 2D textures may be a little pixelated, but it's the same on iPhone.
I don't know if this has been fixed on the recent updates, but the game's real aspect ratio is 3:2, which is the ratio of all iPhones & iTouchs except 5. 5 has a wider screen (about 16:9) so the whole screen looks a bit stretched. All iPads including mini are 4:3, which means the width is less than the game's real ratio, it will appear a bit shrunk. If your iPhone is 4S or earlier, you will get the correct aspect ratio. Don't know if they fixed this issue yet.
You can see the screenshots for iPhone 5 and iPads here: https://itunes.apple.com/app/id575119311
I'm currently playing on my iPad 4 and the graphics aren't stretched it's clear as, not like playing FFI or FFII where it can be zoomed in or out.
I previously said that on iPads it's slightly shrunk, and not stretched. If this is what you get: http://goo.gl/Uznyo then it's shrunk. The real ratio is a little bit wider. It's not a big deal though.