Ok, so now that I am all the way through the fourth gym I'll post my thoughts.
Pros:
Missions- I like how they add a nice extra element to the game on top of the cookie cutter gym-elite four line.
Level scaling- They tend to go up fast as you progress through the story, but the more challenging a game is the better. (Rocket grunts aren't exactly remembered for being elite class trainers lol).
Edge- The game goes out of the way on many occasions to hammer home that you are the villain of the story. Hopefully there won't be any silly twists later that change this.
Music- Some of my favorite themes are in here so no complaints there. Lol
Cons:
Lack of sidequests- The game does feel somewhat linear at times and the massive amount of trainer battles between point A and point B can get repetitive. The addition of some sidequests could help keep the grinding interesting as opposed to just plowing through infinite hikers, campers, etc.
Overall I'm certainly enjoying it so far and I'm definitely interested to see where it goes from here. Good luck man!