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Ok, I see LOTS of potential here, I mean a HUGE amount of programming skill, I just see some flaws, which are pretty easy to solve, at least in my opinion, so here they are, some tips to you.
You need to improve the artwork and animation stuff. A lot. This game would get top scores if the graphics were improved. Haven't you thought about improving your drawing skills, or, if you feel too lazy or unable to improve that, get an experienced artist? Seriously, there is a big lack of art here, and it's a pity this couldn't make to the top 50,or simply get better scores, just because of that, a better design. It's not THAT BAD, but there is room for improvement.
Also, background music in the cities, that would help a lot, and getting some other music for fights, appart from the one you used, which is not bad, anyway. But some variety would be appreciated.
Other than that, I have nothing bad to say about this! The programming is great, and the game is complete and entretaining, I just think it's not very visually attractive after a while. But you'll think about it, right? :P
Well, I must say, overall great work! Looking foward more!