New/changed stuff = cool; lots of bugs/glitches
Still a very fun game and I'm glad you updated the new changes; though I wonder how some of the new changes will fit in from Chapter 1.
There are plenty of glitches, though mostly in combat; such as the screen freeze after each action, etc. I am glad you fixed the "Ailment/Debuff" glitch from Chapter 1 that made it practically impossible to cure them.
I think you should include a little health bar or MP for each monster with their ready bar (if you killed it before) so it can help determine my actions much easier (no point wasting a Limit Break or a Heal when the monsters are nearly dead).
The new additions with the Arena and Timed Run modes are great, and it's good you implemented them as a means for each Chapter with something to do while waiting for the next to be released. If I could use these for my current save files from Chapter 1, I'd be stoked. :)
This still needs some work though; the new "Build" feature is nice, and it allows you to create your own weapons, making Scrap drops actually useful instead of selling for money. Though one other thing you SHOULD implement is a feature that allows you to change any stat on an item and put it into something else to make the general item more suited to the character you want to put it on.
While I notice a few new music themes, the original music from Chapter 1 is kept, and while I like some of the music, some of the others can be...well..."replaced" with something more fitting. But that's just my opinion, I suppose. =/
I mean, other than that, this new installment provides Challenge and Entertainment that the Chapter 1 would have lacked in the long-run.
Recommended for Collection
I can only say keep it up at this point. You're going to generate a game that is legendary on Newgrounds. Sure, this is a Beta, but when it gets up there in the Chapters, you'll be raking in fans all around. Can't wait until Chapter 2, but I'll try to remain patient. :)