Excellent game, but there's a few things...
I'll say it outright: this game is fun even with it's share of flaws.
The gameplay is what you'd expect (which is a good thing). It's been well adapted from the turn-based gameplay into a Tower Defense game, and it works really well. It's fun, and EXP grinding doesn't feel like it's much of a chore because of the hands-off style gameplay Pokémon Tower Defense offers. It doesn't feel butchered at all. I especially love the levels where you can only place certain types of Pokémon at the best spots, such as Mt. Moon 1. I'd be nice it as a more central gameplay element, to keep the player occupied in catching a variety of Pokémon.
Graphics, they're, well, less adapted. Everything's scaled from the games, but not in an orderly, consistent fashion. Some elements are scaled 4x, others 3x, 2x or worst of all, 1.5x. The UI itself could've been better, such as buttons that change colour when the mouse is hovered over them. Some UI elements quasi-overlap, which is not pretty to look at. May I suggest ripping the dialog windows from the games for future versions?
Sound and music is ripped straight from various Pokémon games. Only complaint I have is a lack of consistency, the OST contains various themes, jingles, and sound effects from the first 3 generations of games. I'd suggest only ripping them from FireRed/LeafGreen, just to keep the style.
Some of the levels are just... meh. Many levels following and including Cerulean Gym 2 are just downright unfair. I'd like to use all 6 of my Pokémon at all times, but that's just me. The gameplay just screams to have your Pokémon co-operate with each-other. As for co-operation, is there a possibility of you adding a way to prioritize which moves are used when? I myself and many others hate doing it manually, especially when you have 6 Pokémon out.
Lastly, storyline and dialog. I don't like seeing smileys and bad grammar. I know this is a very minor thing and the game is in Alpha, but still. You'd do yourself a favour to polish it up.
Great work. Keep it up!