Alright so I've just gotten all caught up with the series and I definitely want to be constructive with my criticism so I've divided up my review.
The Good: The story actually is pretty compelling. It's got standard tropes, but that's a good thing. I look forward to seeing the hero's journey to the Elite Four. Like I've said before, I really like how seamlessly this series blends the style of the anime with the style of the games. I especially enjoy the battles and how accurate the moves are so far. Playing the battle is what keeps me watching this series the most.
Criticism 1: One thing I definitely did not like was the flash art part. It really did not match the sprite art style of the series at all. I still find it weird that a talking Pokemon is coming onto TJ but it does seem to be played for laughs which is fine. You should just have it all exactly like it is in the game, including how phone calls work. The more it seems like a "mostly movie except for the major battles" version of the game, the better it will be in my opinion.
Criticism 2: In fact, while it is nice to have voice acting the fact that the voice acting of the main character is weak (no offense) takes away from the series. Maybe hire a professional voice actor to voice the main character? Listening to him in the same scene as someone like Rina really emphasizes the difference in voice acting ability. It sounds more like acting than talking and that's a potential problem. It's something that can be worked on of course if you really want to voice TJ. As long as both of the lead characters sound good, no-one else matters.
Keep up the good work, this series is almost perfect for what it is after a few minor tweaks.