Well, its time for me to crack out my fake 'Super Critique' badge, and talk about what I thought of this series overall. Hopefully the author sees it and perhaps helps him in the future.
Rating: I'll be frank, I was skeptical when I first viewed the animation. I didn't know this series existed until I saw episode 8 on the front page, and when I watched through it, honestly I didn't like it much. It seemed really generic, with everyone having some sort of tragic past of losing all their loved ones and such. But then, though I honestly can't put my finger on why, I became interested in what was going to happen. I ended up watching all the old episodes, questioning what would be next.
I won't sugar coat it, there was a lot of good and bad in this series. In the end, I came to like it, because even though it wasn't really original, it took something that was supposed to be a children's game/show/whatever and turned it into a more serious, mature version. Suddenly enemies didn't just "faint". There was a sense of realism (as far as it would go in a story like this anyway), and characters kind of gained a type of personality that you wouldn't find in a kid's show. Also, as far as animations with sprite work and such, this is one was pretty good. Your skills have evolved quite a bit since your first episode, and I liked the introduction of actual voices. I have to say, though its not perfect, this is a much better production than most people are capable of making. You didn't get shown on the front page for nothing.
Though of course, if I praise your work, I must also criticize it. I must admit, sometimes I felt disconnected from what was happening. Maybe its just me, but occasionally it felt like things just progressed on their own rather than how the viewer spectated it. For example, in the beginning of the series, Garevoir just kinda gave in to TJ when all of the pokeball mechanics were introduced. Actually, I think that happened to a few other Pokemon in the series too. If you remember the tv show from back when you were a kid, you might remember how Ash and Pikachu started out. Pikachu didn't like Ash at all, and he often showed it. He also despised being within a Pokeball and rebelled against it. Though of course as the adventure continued and they experienced many different things together, they eventually became friends in the end. This is how I feel like the relationship between Gardevoir and TJ should have been. You made it kind of feel like the Pokeball was this almighty tool to capture Pokemon like pets and then they were automatically subdued. Maybe thats just me reading into things incorrectly, I'm not sure if others felt that way, but thats kind of how I saw it. Also, going back to the Pikachu reference, I feel like Gardevoir shouldn't really be in her Pokeball very much, if at all. She's supposed to be one of the main characters, perhaps even the mascot for your series, and I thinks she needs to feel that way, especially seeing as how she can talk and such.
I have a few other concerns, one of which being the battle system. Now of course, I remember you said it was something you were kind of tweaking and still learning with, and I can understand that. It just felt kind of clunky, and somewhat forced. I think there should be an option to skip battles in the future (Because, ya know, sometimes people might watch your episode more than once). Aside from that, I think you already know how to fix up the rest of the mechanics for the battle system. I can't really put my finger on it, but I just feel somewhat weird about TJ's personality as well. Maybe its just because he always seems so ambiguous. He's always just like "yeah, okay, that's cool...whatever", to me. Again, maybe that's just me, but he just doesn't really seem relatable. Maybe thats what you were going for, I don't know. If it works for you, then it works.
Hopefully you don't mind my wall of text, I was just trying to be helpful and provide a little more insight than the typical "omigawd, this sucks/is great!" I very much look forward to more.