I think doing away with the trading requirements for the Brawn/Soul Key would be great. Instead of replacing the Brawn Key with the Soul Key, why not put the Soul Key in the chest on the Power Tower Peak that normally has an Herb? I cleared through the tower in an hour in the original version with just an Orochi 4+ with WhiteFire, Shears, LureDance, StopSpell, QuadHits and three moves I never used. I did have to reload saves a few times but that was just for the top two floors. I was seriously disappointed by the Herb.
Also I noticed a lot of confusion between Kagebou and Petibou. Petibou is Warubou's son, but he's just a Warubou. Kagebou is a seperate monster.
I know these are all really about the original hack but I do have ideas for the new one (assuming it's not already complete; if it is then google searches know nothing about it).
First off I think it would be great if monster farm capacity could be increased to more like 50 rather than 30. I spent an embarrassingly large amount of time just trying to decide which ones to get rid of when it was full.
I would keep it so most monsters can be caught in the wild at some point. This was a great feature of your original hack even if some of them had to be bred first.
Make it so using a LogTwig doesn't reset the location of the last warp gate you used a LogTwig on. I was almost literally :banghead:ing when I first played this.
Get rid of about a quarter to a third of the mountains on the edges of the Sky world continents. Also :banghead:ing because of this.
Finally, I would slightly simplify the breeding process for Darkdrium. I started playing this game just to breed Darkdrium then got hooked. I'm only just starting to breed for him, and even after setting out a plan with every monster I will need, it's discouragingly complicated.