The three biggest were the Brothers' War, the Phyrexian Invasion (well, the first one), and the Mending
Ghostly Prison is a very good card for many decks, but since the enchantment angle doesnt do much for Shiko and Narset, it's a fine card to cut
Mister Fantastic, Reed Richards Human Torch, Johnny Storm The Thing, Ben Grimm Invisible Woman, Sue Storm Avengers Balcony BBQ I love supers doing domestic stuff
Wizards experimented with 'symmetric draw' with cards like Secret Rendezvous, where you and another player could both draw cards, but giving your opponent an advantage for something they could probably do themselves feels like a much bigger drawback than other colors
Its more so the fact that many of emeralds cards play better in conjunction with other inks, rather than with themselves