I have, and I've put about 10 hours into it so far.
My first impressions... actually weren't very good. The writing has a lot of really blatant unnecessary exposition and a few pretty glaring plot holes, and Nayuta is just about the blandest main character ever.

In addition, you're constantly being interrupted by lengthy cutscenes that really break the flow of gameplay, there are loads of unnecessary tutorials, there's a weird visual filter that covers the screen with some kind of mesh (presumably to make it look less pixilated, but it's very distracting until you get used to it)... and as mentioned, there's no way to reassign buttons, so you're stuck with O = attack, square = magic, like it or not.
I kept at it, though, because when I *was* able to play an actual stage (which felt like it took FOREVER to get to!), it was super-fun. And as time went on, the quality of the writing improved significantly, the story got more interesting, the ratio of gameplay to cutscene balanced out a lot better and the gameplay itself just got steadily more awesome.
At present, I've passed the "This is disappointing" stage, and entered the "Now that's more like it!" stage. The game feels like a proper successor to Gurumin and Zwei II, with a lot of Ys Seven influences as well. I still have a few complaints with it, and I feel Zwei II did a better job overall with this same formula... and I still don't care for Nayuta as a protagonist... but the platforming in this game is extraordinarily satisfying, the controls are fluid as can be (once you get used to using O for attack and square for magic, anyway), the level designs are absolutely perfect and the game's set pieces and soundtrack are top-notch all the way around (I've already decided that this is the best soundtrack in the whole Kiseki series!).
All in all, it has its flaws (especially during the first few hours), and the story is surprisingly tame and cliched for a game that was touted as being a "story ARPG"... but in the end, I'm really enjoying it. I think anyone who played and enjoyed Gurumin, Zwei II and/or Ys Seven would absolutely enjoy Nayuta no Kiseki, without question. Just get through the slump in the beginning, and you'll be addicted in no time.
(As an aside, though, I can't see how this game relates to any other Kiseki title *at all* so far. It really does feel more like Zwei III or Gurumin II than a Kiseki game. The only references to the main series that I've encountered so far are mira as a form of currency, and selge as a unit of measurement. Literally, that's it!)
-Tom