Regarding VC Events
The VC Mew from the gallery checks as legal for any combination of options Gen I opening options when I load the PKM with my Gen I saves loaded.
I have noticed, however, that if I try to manually generate the VC event Mew, it appears to only check as legal when I select "Physical" AND "Yes" to Gen II learnsets.
I think I read a forum post somewhere from the dev saying that only VC event legality would be included, but I'm not sure if there was a change of heart on that as there was on including Gen I support at all.
Another Issue (Includes crash, exceptions attached)
Additionally, anytime I select anything other than that "Physical" "Yes" combination, certain Pokemon from my physical game check as illegal, some of which seem to me shouldn't appear as such.
Attached are my saves, which haven't been modified after being dumped from my carts.
Now I would intuit that maybe these get flagged for having Gen II learnset moves, but even the Ditto just has transform :s.
So I suppose it is just the fact that these have touched a Gen II cart that they are flagged illegal?
I noticed clicking the legality checker after "viewing" several of these gives a "Legal" message. The ones that fail a second time give errors both about encounter rate and catch rate.
Even with this hypothesis, I have no clue why the Diglett is flagged illegal. Maybe I sent it to Gold for an intermediate trade or something.
In Pokemon Red:
Box 1 - Charizard**, Ditto**, Omastar**, Kabuto*
Box 6 - Diglett
Party - Wartortle*
In Pokemon Blue:
Box 5 - Omanyte*, Kabutops**
Party - Charmeleon*, Blastoise**
* Hatched in Gold
** Sent to Gold for Breeding
BOLD Rechecks as legal
ITALIC Crashes PKHeX when re-checking legality (It's the Omanyte if you missed it)
Pokemon Red.sav
Pokemon Blue.sav
error.txt