I'm not going to get into the end of the story, despite having beaten the game last night because spoilers. I thought it worked out well enough and made sense in context. If you didn't like it, well, differences in opinion are just fine.
I also disagree that combat got boring at high levels with more than 4 enemies. Heck, with too few, it was all one sided and my rogue could one-shot many of them anyhow. That's OK, though, since sometimes it'd be a long battle with annoying mages buffing baddies and such.
My only major issue with the puzzles is how hard to see the buttons can be, especially with the camera being limited in movement. I learned, eventually, to toggle to overhead view, but all too often, it was a bit hard to find those things. WHen I remembered to look for them, at least.

Crafting does need a bit better introduction, but that can be added, I am sure, if the devs agree. As it is, it's a minor issue.