Well, I'd like to say congratulations on the great job. I do hope this will become useful to many.
I tested this briefly in mono and it seems to run ok. There is a small issue with the names containing é instead of e in Pokémon. For one I had to edit the name of the exe on windows for it to be recognized but there was still and issue with the config file. I did not have a suitable save to test completely so I don't know the extent to which that affects things. If it's not too much trouble, might I request that you not use é in the names of the config and the exe?
One again, good job.