As I understand it, there are only two things that affect how
compatible Pokémon in the daycare are: Their Pokédex number and
their OT.
And megas have the same Pokédex number as their regular forms.
But I’ve put a male mega and a female non-mega of the same species
and with different OTs in the daycare, and I’m only getting the
"The two seem to get along very well." message, not the "The two
seem to match perfectly." message.
So, am I missing something? Is there something else that affects
how compatible they are?
They have to be the same species, not have the same Pokedex number.
On this site, Megas are considered a different species to the base
Pokemon, which means they are not compatible.
(There is actually another thing that affects compatibility:
whether the Pokemon are siblings or not; if one of the parents [of
the Pokemon you're using to breed] is the same, then you'll get the
message "The two seem to play with each other, but only as brother
and sister")
Oh, I could’ve sworn I saw someone specifically say that they need
to have the same Pokédex number for the compatibility boost. I
remember thinking it was weird that they said that instead of just
saying they need to be the same species. I wouldn’t know how to
find that post now, though.