Version 2 is great, alot more content added than I was expecting.
my only gripe is that the Juan boss fight seemed very unbalanced, I was lvl 13 all around and was probably under-leveled as I kept running from wild fights but Juan and the bandits did incredibly high damage and took very little damage so I just spammed Tabitha's nuke skill, Bakuretsu!, till they died
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That sounds about correct. Some bosses work more or less as level/gear checks, but there are tricky ways to get around that (Tabitha's Bakuretsu being the most obvious method). Quinn can also force crits to get rid of the two adds quickly. Status effects are also good against bosses since many status effects do % HP damage and most bosses are not immune to paralysis. So there are options if your gear or level is too low.
When it comes to balancing it's hard to hit a good spot since some players skip most of the fights and some fight all, some buy gear constantly while some hoard money, but I try to have the boss fights be somewhere in the middle.