@Are You 18 Now Ive downloaded the most recent .zip from the PKHeX page... I am currently simulating what I did last night just to make sure I am giving you the correct info and advice...
But basically, when you tick the MS .NET 4.6 box inside of Winebottler wintricks, it will go through a process of installing "Microsoft .NET" components. First you will be prompted to perform the Microsoft .NET Framework 2.0 install process. After that you will notice more of these dialogues. They range from MS .NET 2.0 to .NET 2.0 SP1 to .NET 2.0 SP2 to .NET 3.0 etc, etc, etc, etc! --
***PAY ATTENTION- in the middle of the whole process, a dialogue will ask you to restart your pc! Click [restart later] as that isn't relevant to the process.***
--Anyway, It will lead you all the way to Microsoft .NET framework 4.5 and this is where it stops and the Wine application finishes its thing.
Patience is the major component for this process.
in the time that it took me to compose this reply, Winebottler has finished for me, and PKHeX is operational.
Enjoy