Hi, I joined the forums because I wanted to say how thoroughly impressed I was with this concept.
I would like to mention a few things that I've noticed, as I've already found a few problems; things you might want to work on.
Problem 1: Professor Oak's Laboratory
The game asks you to go see the third Pokéball, and once you find out it's empty, the game moves you down, to the left, and up, to speak to Oak again. However, if you are above the table, like I was to begin with, it will keep trying to move you down indefinitely. The only solution is to reset the game.
Problem 2: Viridian Gym
When you go to the Viridian Gym early in the game, it tells you that it's locked, then moves you down. Unfortunately, the game then locks you out of moving. You can press c to bring up the menu, and whatnot, but the arrow keys become useless. The only solution is to reset the game.
Problem 3: Pewter Gym
I don't actually know why, but I've just entered Brock's Gym after entering Pewter City for the first time (I healed my Pokémon at the center first), and the entire game just crashes (Windows tells me that it apologizes, but Game.exe has suffered an error and must be closed).
Problem 4a: Music Looping
Music looping is fantastic, don't get me wrong, but you need to be able to separate introductory music from the looped music. The notes that introduce a battle aren't repeated in the games, and it can get confusing listening to it again after being so used to it meaning that a new battle is starting.
Problem 4b: Missing sound effect
You're missing the sound effect of running feet/sweeping that happens when you successfully run from an encounter.. I've tried locating it online, but haven't been successful yet -- if I do find it, I'll link the file here.
Problem 5: NPC Walking: Sometimes, they can walk directly in front of doors / the only exit, and while they do move eventually, it can get a bit frustrating.
Don't take this to mean that the game is bad -- quite the contrary, I'm looking forward to getting more than an hour into the game (yeah, I have a lot of criticism for such short playing time), but I think that these things could be improved for later on, and for future players.
Keep up the good work, and if there's anything I can do, let me know! I can program in Visual BASIC .net, Java, and Wolfram Mathematica (none of which, I assume, are particularly useful to you), but I can, if needed, consult, and perhaps take a look at some of the code to optimize the methodology, if you would like it.
Again, keep it up :)
EDIT: Apparently, I can't walk into the museum in Pewter City, either.