Wow, this is amazing!
I've seen a lot of RPGs on Newgrounds that are nothing more than crap, but this is gold! It works very well and has a lot of promise! A few issues, though:
1. Sprite animations are laggy.
2. Sometimes during conversations, an extra, blank text box will appear when someone is done talking, before moving on to the next speaker.
3. X's melee move has multiple white flashes, making it confusing to get a timed attack. Perhaps using a different color or a larger/different flashing effect.
4. Some sprites look kind of blocky or choppy due to enlarging. Perhaps using anti-aliasing or vectors would help? (Although I don't know too much about those...)
All in all, this is a great game, and while it has some room to improve, it is very fun and the series shows a lot of promise.
Also, a suggestion: Maybe adding a bar akin to the ATB Gauge in the FINAL FANTASY series to let you know when you can attack or how long you have to wait. If there is already one, then I missed it, and in that case, oops.