There are now (well, have been for a while) multiple ways to evolve
a Pokémon from its unique parent, so the current schema wasn't working.
The parent Pokémon has moved back to the main pokemon table, and
pokemon_evolution has grown an artificial primary key.
New evolution methods for Milotic, Leafeon, Glaceon, Magnezone, and
Probopass have been added.
Chimecho does not have gender differences; its Platinum and HG/SS second-
frame female backsprites have one hand posed a little differently, but
no actual design differences.
Torchic does count even though the only difference is a single-pixel dark
speck on the male's rear; the speck was carried over into B/W even though
the backsprites were entirely redone, so I'm guessing it either was
deliberate or has ascended into canon via "let's throw it in anyway."
The step counts we had weren't even good estimates. To hatch an egg
uninterrupted takes (counter + 1) * 255 steps in gen IV; what we had
was counter * 256.
Phione and Manaphy have different counters, as do Croagunk and Toxicroak
for some reason, so they're associated with individual Pokémon now,
rather than entire evolution chains. Double-checked with Pearl,
Platinum, and SoulSilver; there were no differences between the three,
aside from the alternate forms introduced in Platinum.
Every flavor page should work with no missing sprites. Save perhaps for
Unown, because I honestly don't have them.
Every sprite exists as ###-form.png. There is also still a ###.png,
containing a reasonable default form, so people who don't give a crap
about this mess can just use the numbered sprites. Beta forms should
now all be ###-beta.png.
Form groups now have a notion of "in-battle", which is used to hide
overworld sprites when appropriate.
Form sprites have a first-class sense of being a default or not, too.
Deoxys is... well, let's not talk about Deoxys. Deoxys is fixed.
Only the version group a forme actually exists in now has any moves for
that forme.
In addition, Deoxys formes were not showing any gen 3 moves at all
previously, because they were marked as only existing in gen 4. This
has been fixed.