Interesting idea
Good points:
I think the general idea behind this game is very good. I've played many tower defense games before, but this one does feel different from most others. The level up and evolution system of the Pokemon games is integrated very well into this tower defense game. Also, I was expecting that the game would be very glitch-y and needed lots of improvements, but during play I found out that it actually works very well. There are probably some bugs still left somewhere, but so far I haven't noticed anything noteworthy, so good job on the programming.
Finally, I thought your first version was kinda short with only four levels or so (up to the Pewter Gym), but I see you already improved on that and updated the game. I thought you were gonna release a new submission that would somehow take the save file from this game and use it there (via cookies or something), but you simply updated this one. I think that's the best way to do it, and you got plenty of filesize left to make the game bigger.
Bad points:
The lay-out isn't that pretty. In some screens it's really a bit simplistic with a pure black background and a standard text font. It would be good if you could improve a bit on that. Especially the text font shouldn't be too hard to improve on (just find something prettier). Secondly, I don't think the story was all that interesting, so I skipped through it most of the time. Not a big deal though, the gameplay makes up for it in my opinion.
Lastly, and this is actually more of a tip, I don't think it's necessary to include every single Pokemon from the first generation and synchronize their movesets and all. Of course it's great if you can do that, but I got a feeling that it's a shitload of work for you while the game could be just as awesome without including the uninteresting Pokemon. I don't know what your future plans are with the game, but I doubt anybody would be interested in having a fucking Bellsprout on his team for example.
Overall 9 out of 10, 5 out of 5. The prime reason I didn't gave it a 10 out of 10 is due to the simplistic graphics and lay-out. I think there's plenty of room for improvement there still. For the rest it's an interesting game in my opinion and I hope you will continue this project and finish it someday. Good job.
~Auz