Let's see what non-standard things I can point out that I feel are fairly unique to PokeGen that also exist in your program, and could be done differently.
Two "save" entries in the file menu. (As in one specifically related to Pokemon data and one specifically related to save files.)
Escape sequences with no preceding x or 0x to indicate hexadecimal.
Referring to the Pokemon with the word "species", which I don't think is that common, and is more of my own personal preference.
Toggleable options in a menu by themselves, rather than a dialog.
Using the text "Black (2)/White (2)"... come on... you really did that on your own?
A list of version changes in the program, rather than external.
I can't deny that all of these things really can be coincidental. I'm just skeptical of that. If you're really not using PokeGen as a reference, then just ignore my posts. Otherwise, at least admit to it. (And come up with more uniqueness, while you're at it.)