Hello!
I will try to explain me, but I'm spanish and maybe I use some bad words
I think that PKHEX is wonderful but maybe I miss some features,
One of them is the button that you can see in PokeGen, wich allows you to use your own TID/SID of your savegame. You push the button and automatically the poke gets your TID/SID/OT.
Other feature that I think that could be interesting is, "mass" editor, I mean: You choose 5/6/7/8/9... (Or an entire box) and you can change the Level for all (for example), or the Country for all...
This feature can be "injected" on the main program or maybe in the Box Data Report and edit in this place.
I hope that you consider these features
Thanks for reading and sorry for my English