sorry for the slow replies, just been occupied with other stuff lately.
Oh and another thing I wanted to mention. Is it possible to edit the max PP a puppet can use to increase stats?
this requires editing the save file. there is a hard-coded check to prevent you from increasing EVs above 64 each or 130 total via the in-game UI, but you can edit your save to increase EVs up to +255 each. this can also be done to trainer puppets (infact older versions of the randomizer did it by accident).
i'm not sure if there are any other hard-coded checks that prevent EV editing from actually being effectual in-game though, particularly for EVs over 64 (iirc it does check that sort of thing for netplay).
you can use dabomstews
save editor if you just want to edit your own puppets EVs. the randomizer could be made to allow higher EVs for trainer puppets, but it can't raise the cap on player puppets.
Would it be possible to randomize the appearance rates for puppets? Or the number of different species in each area? Like having one area with 10 types of puppets with roughly 10% chance for any of them, but the next area only has 3 and two of them are 5% chance to appear, while the third has a 90% chance. Or is that stuff all hard coded?
all of that is possible, but i've not tested it much. as far as i can tell each puppet has a "weight" which determines its encounter rate relative to the other puppets. i would expect the percentage to be the weight divided by the sum of weights, and while that mostly seems to be the case so far, i can't guarantee there isn't any other weirdness.
i've made a beta build that adds randomization for both encounter rate (separate option) and number of puppets in an area (applied to the normal wild puppet randomization) and an option to either randomize puppet cost or set them all to 120 cost (in the form of a 3-state checkbox, click twice to set the latter option).
the wild puppet checkbox has also been turned into a 3-state, with the 3rd state being style only. additionally, the "catch locations" file will now display expected encounter rates.
the OP will not link to this since it's largely untested. you can get it
here if you'd like to try it out.
note that a number of areas have multiple sub-areas that share the same name (e.g. youkai mountain). these are now numbered in brackets "Youkai Mountain [2]" to avoid confusion.