I just finished the game yesterday, and enjoyed it immensely!
Things I really loved and felt were quite unique:
1) The wide variety of transportation methods, especially the runes, which were available from the beginning. One of the things I hate is continually backtracking through places to get from point a to point b. And, as others have mentioned, there were very unique modes of travel like the wale and griffin.
2) The skill pill system. As others have mentioned, this system was extremely unique and I loved it.
3) The monster visibility. I hate invisible monsters because it seems like you take a few steps, have to battle, take a few steps. . . bleh. It just gets very old, but that wasn't a problem in this game.
4) Loved the auto battle. Sometimes, especially when battling lower level things, I just get sick of going through the fight option for each character, so the auto battle was great.
5) I really enjoyed the pop culture references!
6) The puzzles. I loved the fact that the puzzles were not so difficult that I wanted to tear my hear out! I don't mind puzzles in rpgs, but I usually am more interested in the story, so I hate it when I have to keep retrying puzzles before I can progress (the same goes for grinding for hours just to get a little snippet of story!).
Things I felt could have been tweaked a tiny bit
1) The maps and villages/places to visit were a little sparse. But, that could just be me, personally, because part of what I enjoy so much is exploring and also the conversations with other characters, which both seemed a bit more limited
2) The story itself was a little sparse, at times. It felt like there was a lot of backstory missing and that characters could have been fleshed out a bit more. Also, I would have liked more character and npc interaction. Instead, it often felt like one characters was "telling" everything, rather than finding out things through character interaction.
3) I liked the "twists." I know some people hated the fact that if you chose the wrong option, Harry Potter disappeared (I also accidentally killed off Loyola (I think that was her name) and couldn't go back and get her. I think you should include more of this type of scenario in future games--the option a, b, or c, which leads to different outcomes. I like the surprises, and also it leads to more replayability.
4) I think you could also make a lot of the skill pills, at least the higher level ones, more limited. I know there were a few like that, but overall, I just kept giving everybody all of them. Yes, I know Maureen had no MP, but I battled those horses until I got him 20 MP upgrades, just to see what he could do with magic I think, if you did this, it would make people have to really think about which characters should have which skills, and also even which characters are best for the party.
I would say, though, that even though the story, for me, was a little disappointing (I was an English major, what can I say ), the battle system, the ability to avoid certain monsters--at least until you had leveled up a bit-- and the skill pill option really made this an enjoyable game!